The ID Update

Anyone attempting to swat a fly will become aware of its remarkable aerodynamic capabilities. Its speed of response and ability to change direction abruptly far exceed our own powers as pursuers. The flight of insects has received considerable attention from researchers and some recent work was stimulated by the recognition of a gap in knowledge. The scientists realized that the previously-studied flight control system involving vision cannot be the explanation for how flies maintain stability in the face of unpredictable short disturbances.

"Corrective behavior often takes advantage of vision. For fruit flies, however, reaction time to visual stimuli is at least 10 wingbeats, so these insects must employ faster sensory circuits to recover from short time-scale disturbances and instabilities."

To study how fruit flies recover from in-flight disturbances, researchers glued magnetic pins to the insects' backs and zapped them with a magnetic field. This fly has a 1.5 mm pin on its back and is held in place by the tip of a sewing needle. (Credit: Wang, Cohen and Guckenheimer labs, Source here)

The experimental work required the research team to abandon ideas of tethering insects or imposing other restrictions on flight behavior. They needed to observe insects in free-flight.

"To probe this fast control strategy, we devised an experimental method that imposes impulsive mechanical disturbances to flying insects while allowing us to measure relevant aspects of flight behavior. We first glue tiny ferromagnetic pins to fruit flies and image their free flight using three orthogonally oriented high-speed video cameras. When a fly enters the filming volume, an optical trigger detects the insect, initiates recording, and activates a pair of Helmholtz coils that produce a magnetic field. The field and pin are both oriented horizontally, so the resulting torque on the pin reorients the yaw, or heading angle, of the insect. We then use a new motion tracking technique to extract the three-dimensional body and wing motions."

What they observed is that prior to the perturbation (which lasted 5ms, or about one wingbeat period), the wings beat symmetrically. After the magnetic torque was applied, 3 wingbeats were needed for the control system to respond, and then "asymmetries in the wing motions appear for about five wingbeats, indicating the insect is actively generating corrective torque". For small perturbations, the insects correct "nearly perfectly", whereas larger perturbations - although corrected to some extent - lead to permanent changes in heading.

"The accuracy of the recovery indicates that a refined control strategy underlies the response of fruit flies to in-flight perturbations. To reveal this strategy, we construct a physics-based model of the observed behavioral response."

Body motions are detected by the halteres: "small vibrating organs [. . .] that act as gyroscopic sensors. Anatomical, mechanical, and behavioral evidence indicates that the halteres serve as detectors of body angular velocity that quickly trigger muscle action." With this model, the halteres have a nonlinear response consistent with vibratory gyroscopes, so sensor saturation explains "why fruit flies are unable to accurately recover from strong perturbations". The control system design principles are as follows:

"These findings suggest that these insects drive their corrective response using an autostabilizing feedback loop in which the sensed angular velocity serves as the input to the flight controller. [. . .] [T]he velocity is sensed by the halteres, processed by a neural controller, and transmitted by the flight motor into specific wing motions that generate aerodynamic torque."

Halteres are remarkable organs and unique to the Diptera. The research raises questions about other autostabilization techniques found in the natural world and how such systems can be incorporated into flying robots.

"Flight control principles uncovered in this model organism may also apply more broadly, and this work provides a template for future studies aimed at determining if other animals employ flight autostabilization. The control strategies across different animals are likely to share common features, because the physics of body rotation is similar across many animals during flapping-wing flight. Additionally, animals that lack halteres may use functionally equivalent mechanosensory structures such as antennae. Finally, the control architecture of the fruit fly offers a blueprint for stabilization of highly maneuverable flapping-wing flying machines."

These design principles were incorporated by intelligent agents into aeroplanes very early in their history (further information is here). It is now apparent that flying insects got there first! In evolutionary terms, we have here a good example of convergence. Since these control systems represent complex specified information (with the greater complexity found in the insect control system), intelligent agency should be invoked in both cases.

"For fixed-wing machines, the need to overcome instabilities spurred the invention of autostabilizing systems by 1912, only 9 years after the Wright brothers first manually controlled airplane flight. The development of such automatic steering systems also led to the first formal description of proportional-integral-derivative control schemes and advanced gyroscopic sensor technology. The fruit fly's autostabilization response is well-modeled by a simple PD scheme that receives input from gyroscopic halteres, and, like airplanes, uses fine adjustment of wing orientation to generate corrective torques. Roughly 350 million years after insects took flight, man converged to this solution for the problem of flight control and joined animals in the skies."

Discovering the flight autostabilizer of fruit flies by inducing aerial stumbles
Leif Ristroph, Attila J. Bergou, Gunnar Ristroph, Katherine Coumes, Gordon J. Berman, John Guckenheimer, Z. Jane Wang and Itai Cohen.
Proceedings of the National Academy of Sciences, 2010, 107:4820-4824 | doi:10.1073/pnas.1000615107

Abstract: Just as the Wright brothers implemented controls to achieve stable airplane flight, flying insects have evolved behavioral strategies that ensure recovery from flight disturbances. Pioneering studies performed on tethered and dissected insects demonstrate that the sensory, neurological, and musculoskeletal systems play important roles in flight control. Such studies, however, cannot produce an integrative model of insect flight stability because they do not incorporate the interaction of these systems with free-flight aerodynamics. We directly investigate control and stability through the application of torque impulses to freely flying fruit flies (Drosophila melanogaster) and measurement of their behavioral response. High-speed video and a new motion tracking method capture the aerial "stumble", and we discover that flies respond to gentle disturbances by accurately returning to their original orientation. These insects take advantage of a stabilizing aerodynamic influence and active torque generation to recover their heading to within 2 deg in less than 60 ms. To explain this recovery behavior, we form a feedback control model that includes the fly's ability to sense body rotations, process this information, and actuate the wing motions that generate corrective aerodynamic torque. Thus, like early man-made aircraft and modern fighter jets, the fruit fly employs an automatic stabilization scheme that reacts to short time-scale disturbances.

by Denyse O'Leary
ARN correspondent

Here's an interesting article in New Scientist by Bob Holmes on a new approach to how animals become separate species ("Accidental origins: Where species come from", March 10, 2010):

Everywhere you look in nature, you can see evidence of natural selection at work in the adaptation of species to their environment. Surprisingly though, natural selection may have little role to play in one of the key steps of evolution - the origin of new species. Instead it would appear that speciation is merely an accident of fate.

So, at least, says Mark Pagel, an evolutionary biologist at the University of Reading, UK. If his controversial claim proves correct, then the broad canvas of life - the profusion of beetles and rodents, the dearth of primates, and so on - may have less to do with the guiding hand of natural selection and more to do with evolutionary accident-proneness.

[ ... ]

"When it works, it works remarkably well," he says. "But it only works in about 6 per cent of cases. It doesn't seem to be a general way that groups of species fill out their niches."

Then Darwin's theory just barely makes it to statistical significance, conventionally given as 4 per cent.

The otherwise most informative article is marred by the constant need to claim that Darwin was not wrong - but obviously, if Pagels is right, Darwin was indeed wrong, and so are all the people fronting his cause. Natural selection acting on random mutation was, precisely, Darwin's proposed mechanism.

No one supposes that natural selection doesn’t occur. But is it the main driver of new species, as Darwin thought, and Pagels doubts?

Pagels dances very nervously indeed around that point (presumably from fear of joining the Expelled, given that his genome research has failed to back Darwin up.

So, for a free copy of Expelled, which details what happened to a variety of people who questioned establishment Darwinism, based on its failures of evidence, and provide the best answer to this question: What do you think of Pagels’s evidence? Is it critical? Is he just blowing smoke? Will he be forced to recant?

Here's where you enter, which you do by posting a comment, 400 words or less. If you are new to Uncommon Descent, you will need to sign up.

Here are the contest rules, not many or difficult. The main thing is 400 words or less. Winners receive a certificate verifying their win as well as the prize. Winners must provide me with a valid postal address, though it need not be theirs. A winner's name is never added to a mailing list. There is no mailing list. Have fun!

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

The mollusc, known as the scaly-foot gastropod, has been known for about a decade. It was discovered living in the deep sea near the Kairei Indian hydrothermal vent field on the Central Indian Ridge. The natural environment for the animal is harsh. There are extremes of temperatures, high pressures and high acidity levels that can easily damage shells of calcium carbonate. Brachyuran crabs live in the vicinity and these "are known to compress gastropod mollusc shells between their chela" with loads of up to 60N.

"To understand how the valiant gastropod holds up to these trials, Christine Ortiz of MIT and her colleagues used nanoscale experiments and computer simulations to dig in to the shell's structure. Many other species' shells exhibit what Ortiz calls "mechanical property amplification," in which the whole material is hundreds of times stronger than the sum of its parts."

The scaly-foot gastropod uses a unique trilayered shell to protect itself from hazards. (Image credit: Anders Waren, Swedish Museum of Natural History. Source here)

Most exoskeletal structures are technically known as multilayered composites. The parameters are the layer thicknesses, the nano- and microstructure of each layer, the number of layers, the sequence of layers, etc. Each species appears to have its own resultant profile.

"Design, inspired by nature, of engineering materials with robust and multifunctional mechanical properties [i.e., those which sustain a variety of loading conditions] is a topic of major technological interest in a variety of civilian and defense applications. Here, we identify the design principles of the shell of a gastropod mollusc from a deep-sea hydrothermal vent [order Neomphalina, family Peltospiridae, species Crysomallon squamiferum]. This system has a trilayered structure unlike any other known mollusc or any other known natural armor, with a relatively thick compliant organic layer embedded between two stiffer mineralized layers, an outer iron sulfide-based layer and an inner calcified shell."

The outer layer is about 30 micrometres thick and is mineralised: it contains iron sulphide particles (greigite, Fe2S4). This gastropod is the only metazoan known to employ iron sulphide as a skeletal material. The middle layer is about 150 micrometres thick and is thought to be the periostracum (the template for shell mineralization, providing protection against corrosive and dissolutive marine environments, and also chemical protection from boring organisms). The inner layer is composed of aragonite that is itself layered:

"[It] possesses a gradient layer [. . .] with a typical crossed lamellar layer (CLL) microstructure (approximately 50 [micro]m thick), followed by a relatively thick layer also with a CLL microstructure (approximately 200 [micro]m thick, followed by a thin prismatic layer (PL) on the inner surface of the shell (approximately 1.5 [micro]m thick)."

This structure has been studied empirically and modelled. Simulations were performed to understand how the shell responds to impacts and applied loads. There are too many details to document here.

"It is interesting to see how C. squamiferum has created these additional different protection mechanism compared to other gastropod molluscs by using materials plentiful and specific to the deep-sea hydrothermal vent environment, i.e., vent fluids rich in dissolved sulfides and metals.
The design principles of the trilayered shell of C. squamiferum exhibit many aspects that are different from the highly calcified shells of typical gastropod molluscs or any other natural armor. Each material layer serves distinct and multifunctional roles leading to many advantages."

Design principles have emerged from this research. The authors have found new design features leading to enhanced functional performance. "Each material layer serves distinct and multifunctional roles leading to many advantages". They point out that design principles are extremely important because there are so many variables: "The design space for synthetic multilayered structural composites for protective applications is enormous". The great merit of biological systems is that they provide a chart to steer through this space. However, the authors attribute design in biological systems to an "evolutionary process".

"Biological systems, such as the one described here, greatly reduce the engineering design space since efficient threat-protection design concepts have emerged through the lengthy evolutionary process that fulfill the necessary functions and constraints."

The problem with this evolutionary framework is that it has no empirical validity. We have no warrant for explaining design principles via evolutionary processes. The authors explain that they do not know whether the observed design "represents an advanced functional adaptation as an antipredatory response or an exaptation (i.e., a trait that evolved to serve one function, but subsequently and simultaneously may serve other functions)". This comment is, unfortunately, entirely typical of the culture prevailing in science produced by philosophical materialism. Evolutionists have supreme confidence in their theoretical framework, but do not seem to see the need to constrain theory by reference to empirical data. Observed adaptations do not demonstrate the emergence of design concepts. The only sources of design concepts that we know of are intelligent agents. Replacing the culture of materialism by one that integrates information inputs with physics and chemistry is long overdue.

With this alternative culture, paragraphs like the following take on a new richness of meaning:

"In particular, the efficient natural armor structural system described here sustains both mechanical loading, as well as thermal fluctuations with inherent mechanisms to prevent catastrophic failure. The multimaterial, trilayer design and advantageous curved geometry enables structural stiffening, reduction of radial displacements, penetration resistance, and stability during thermal impulses even with the presence of large mismatches between constituent materials. Trilayered sandwich composite designs have had limited use in military applications, and the concepts reported here could lead to bioinspired improvements and broader applicability and improved performance for human, vehicle, and structural armor."

Protection mechanisms of the iron-plated armor of a deep-sea hydrothermal vent gastropod
Haimin Yao, Ming Dao, Timothy Imholt, Jamie Huang, Kevin Wheeler, Alejandro Bonilla, Subra Suresh, and Christine Ortiz
Proceedings of the National Academy of Sciences, January 19, 2010, vol. 107, no. 3, 987-992 | doi:10.1073/pnas.0912988107

Abstract: Biological exoskeletons, in particular those with unusually robust and multifunctional properties, hold enormous potential for the development of improved load-bearing and protective engineering materials. Here, we report new materials and mechanical design principles of the iron-plated multilayered structure of the natural armor of Crysomallon squamiferum, a recently discovered gastropod mollusc from the Kairei Indian hydrothermal vent field, which is unlike any other known natural or synthetic engineered armor. We have determined through nanoscale experiments and computational simulations of a predatory attack that the specific combination of different materials, microstructures, interfacial geometries, gradation, and layering are advantageous for penetration resistance, energy dissipation, mitigation of fracture and crack arrest, reduction of back deflections, and resistance to bending and tensile loads. The structure-property-performance relationships described are expected to be of technological interest for a variety of civilian and defense applications.

See also:

Grossman, L. Snail In Shining Armor, Science News, February 13th, 2010; Vol.177 #4 (p. 13)

Stephen Meyer responds to Francisco J. Ayala's review of his book Signiture in the Cell.

More...

A great example of ID...and far less complex than the working inside a human cell, as shown in THIS ANIMATION.

and in Unlocking the Mystery of Life

Here is the Rube Goldberg machine...

In the EnterpriseBlog, Jay Richards comments on the story in the New York Times about the linking of climate change and evolution.

Richards opines...there are budding initiatives in state legislatures and boards of education to encourage or require balance in classroom discussions of global warming. The point of the piece, though, is to connect the teaching of evolution to the climate change debate:

Critics of the teaching of evolution in the nation's classrooms are gaining ground in some states by linking the issue to global warming, arguing that dissenting views on both scientific subjects should be taught in public schools.

Now when I read anything on the environment in the New York Times, I try to keep a couple of deconstructionist qualifiers running in the back of my head: "This is what the New York Times wants me to believe about the issue" and "What are they trying to accomplish with this piece?" I know it's cynical, but when it comes to environmental stories, I just don't trust New York Times reporters to keep it straight.

Some things they want to accomplish with this piece:

More...

A fossil that was celebrated last year as a possible "missing link" between humans and early primates is actually a forebearer of modern-day lemurs and lorises, according to two papers by scientists at The University of Texas at Austin, Duke University and the University of Chicago.

In an article now available online in the Journal of Human Evolution, four scientists present evidence that the 47-million-year-old Darwinius masillae is not a haplorhine primate like humans, apes and monkeys, as the 2009 research claimed.

They also note that the article on Darwinius published last year in the journal PLoS ONE ignores two decades of published research showing that similar fossils are actually strepsirrhines, the primate group that includes lemurs and lorises.

More...

Well known theologist, R.C. Sproul, interviewed Stephen Meyer, author of Signature in the Cell: DNA and the Evidence for Intelligent Design, on philosophy, evolution, education, Intelligent Design, and more.

The GospelCoalition has the link. Scroll down to Justin Taylor's March 5 post.

Click HERE.

This debate was held at Indiana University.

Craig's analysis, as usual, was beautifully precise and accurate.

For the debate, click HERE.

Spider silk has been an active area for biomimetics research for several years. Spinoff companies have been launched in anticipation of commercial gains. However, despite the enthusiasm and commitment of research staff, the prizes are still elusive. Whilst the main goal is to produce fibres that are as strong and as flexible as spider silk, there are other aspects of the natural material that have attracted the interest of researchers. One of these concerns the ability of webs to be a site for dew collection.

"When Lei Jiang first observed the phenomenon, he was intrigued. "How does that happen?" he wondered. After all, he says, "if you took a human hair, water would not stick to it like that". His initial curiosity led to an almost five-year-long study. The findings could have implications for the design of materials for water collection and for the efficiency of chemical reactions."

Spider silk manipulates water with skill (source here)

Not only do webs attract dew, the droplets are able to hang stably on the silk fibres. This suggests the presence of a microstructural mechanism. All polymeric fibres have a microstructure and spider silk is no exception. SEM images reveal a series of amorphous regions (called puffs) and crystalline regions (called joints). The nanofibrils are highly hydrophilic: enhancing wettability and favourable for condensing dew. The puffs have a very open structure and are semi-transparent in images. However, when water starts to condense, the puffs shrink - first to "opaque bumps" and then to "spindle-knots". As they shrink, tiny water droplets coalesce to form larger drops with movement from joints to spindle-knots.

"Further work revealed that movement of the droplets towards the knots is directed by two forces acting together: the force generated by a gradient of surface energy on the fibrils and the one produced by the spindle shape of the knots. "This is quite different from other reported surfaces, on which drops are driven just by individual forces," says Jiang."

These findings are stimulating human invention. The research paper reports success with nylon filaments that are coated with a hydrophilic material that dries in tiny knots similar to those found in spider silk. The goal now is to produce something of commercial value.

"These observations clearly show that our artificial spider silk not only mimics the structure of wet-rebuilt spider silk but also its directional water collection capability. We therefore anticipate that the design principles uncovered and implemented in this study will aid the development of functional fibres for use in water collection and in liquid aerosols filtering in manufacturing processes."

Why does the spider produce a web with dew-gathering potential? "The researchers are unsure of why the spider has evolved to possess this ability. "It could be for its drinking activities, or it could be to refresh the web structure to make it stronger and stickier for prey," Jiang told physicsworld.com." Magdalena Helmer wrote a short News & Views piece on "Dew catchers", saying: "spiders don't need to look for water because the silk fibres that they spin are highly efficient at collecting it from moist air". However, direct evidence of functionality is lacking. There is considerable scepticism that spiders make any use of dew-gathering.

"But Fritz Vollrath, who studies spider silk at Oxford University in the UK, disagrees with Jiang's theory. He thinks spider silk has to be dry to function. 'If I am correct, then the authors are studying an artefact, which is still interesting, although it has no biological function,' says Vollrath. [. . .] Brent Opell, a spider expert at Virginia Tech in Virginia, US, is equally cautious about the results, although he says the experimental work is sound. 'The implication that [capture] threads have evolved to harvest moisture is not the view of most arachnologists,' he says."

Is there an ID perspective on this? Wherever researchers recognise "design principles" in the natural world, the answer is, of course, 'yes'. The presumption with ID is that design features imply functionality, whether or not we know the details. Dew gathering is a unique and remarkable feature of spider silk simply because other fibres do not display such behaviour. The authors comment:

"We observed such directional water collection behaviour only with wetted silk fibres (that is, wet-rebuilt silk) from the cribellate spider Uloborus walckenaerius; in contrast, silkworm silk and nylon fibres with a uniform structure did not exhibit the directional water collection phenomenon."

Whether evolutionists can explain 'how the spider came to gather dew' is more uncertain. Even with functionality identified, perfecting this highly engineered system makes it most reasonable to infer intelligent, rather than natural, causation.

Directional water collection on wetted spider silk
Yongmei Zheng, Hao Bai, Zhongbing Huang, Xuelin Tian, Fu-Qiang Nie, Yong Zhao, Jin Zhai & Lei Jiang
Nature, 463, 640-643 (4 February 2010) | doi:10.1038/nature08729

First paragraph: Many biological surfaces in both the plant and animal kingdom possess unusual structural features at the micro- and nanometre-scale that control their interaction with water and hence wettability. An intriguing example is provided by desert beetles, which use micrometre-sized patterns of hydrophobic and hydrophilic regions on their backs to capture water from humid air. As anyone who has admired spider webs adorned with dew drops will appreciate, spider silk is also capable of efficiently collecting water from air. Here we show that the water-collecting ability of the capture silk of the cribellate spider Uloborus walckenaerius is the result of a unique fibre structure that forms after wetting, with the 'wet-rebuilt' fibres characterized by periodic spindle-knots made of random nanofibrils and separated by joints made of aligned nanofibrils. These structural features result in a surface energy gradient between the spindle-knots and the joints and also in a difference in Laplace pressure, with both factors acting together to achieve continuous condensation and directional collection of water drops around spindle-knots. Submillimetre-sized liquid drops have been driven by surface energy gradients or a difference in Laplace pressure, but until now neither force on its own has been used to overcome the larger hysteresis effects that make the movement of micrometre-sized drops more difficult. By tapping into both driving forces, spider silk achieves this task. Inspired by this finding, we designed artificial fibres that mimic the structural features of silk and exhibit its directional water-collecting ability.

Making the paper: Lei Jiang
Nature, 463, 586 (4 February 2010) | doi:10.1038/7281586a

Abstract: Spider silk structure holds secret to catching water as well as flies.

See also:

Birch, H. How spider silk soaks up water, Chemistry World (3 February 2010)

Dacey, J. Spider web inspires fibres for industry, physicsworld.com (3 February 2010)

Helmer, M. Dew catchers, Nature, 463, 618 (4 February 2010) | doi:10.1038/463618a

by Denyse O'Leary
ARN correspondent

I see where Discovery Institute has put up a podcast with me, on "Is the Brain Just an Illusion"?

This must be one of the ones I did in Seattle in 2007, when they asked me to come and explain the book.

What I always ask is, "If the brain or the mind are an illusion, whose illusion are they?"

This question is modelled on the Jewish zen: "If the mind is an illusion, whose arthritis is this?"

On this episode of ID The Future, Anika Smith interviews science writer Denyse O'Leary about her book, The Spiritual Brain: A Neuroscientist's Case for the Existence of the Soul.

In the book O'Leary and her co-author Mario Beaurogard, neuroscientist and Associate Professor at Université de Montréal, explore the question of whether or not the mind is an illusion as materialists believe. The Spiritual Brain looks at whether religious experiences come from God or are merely the random firing of neurons in the brain. Drawing on his own research with Carmelite nuns, Beauregard shows that genuine, life-changing spiritual events can be documented. He and O'Leary offer compelling evidence that mind creates matter, rather than matter creating mind.

Listen here. By the way, I always call myself the co-author and recognize neuroscientist Mario Beauregard of the Universite de Montreal as the lead author.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

On the supposed evolutionary origin of religion:

Did you know that: Religion is good for you; also, Religion is bad for you; also, Religion makes no difference; also, Religion can be explained by a God gene, or a meme, or part of the brain . . . or whatever the editor of your local paper's "Relationships" section will buy for this weekend's edition?

You didn't know any of those things? Aw, no surprise. But never fear: One outreach of the new atheist movement, currently making its way around the lecture rooms of the nation, is the academic attempt to account for religious belief, and to do so on any basis whatsoever, except one.

We will get to that forbidden one in a moment. First, let's look at the permitted ones.

[ ... ]

Okay, so what is missing from this picture?

First, common sense: Suppose I told you that flossing your teeth (1) helped; (2) didn't help; (3) made no difference; (4) can be explained by . . . (choose an option). What would you reasonably conclude about the state of the evidence?

Go here for the rest.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

Robert Deyes
ARN Correspondent

The Spanish Paseos Por La Naturaleza (A Walk Through Nature) series continues with an exploration of catalytic RNA within the larger context of the RNA world. Pulling together key lines of evidence from molecular biology, this installment builds a linchpin case against the fragile trusses of naturalistic causation.

The Paseos Por La Naturaleza series aims to further strengthen the global influence that the Intelligent Design movement already enjoys and raise awareness of important academic resources that are today challenging orthodox Darwinism and revitalizing the call for a fresh perspective on scientific discourse.

The third installment can be found at:
El ARN catalitico - un catalizador indigno de una discusion seria acerca del origen de la vida (See also OIACDI)

Two research psychologists have contributed an Opinion paper based on the empirical finding "that individuals presented with unfamiliar moral dilemmas show no difference in their responses if they have a religious background or not". The data used was obtained from an online web questionnaire which is open to any volunteer participants (including myself). Findings are reported elsewhere and in their Opinion paper the authors provide only a summary:

"These studies, carried out using the web-based Moral Sense Test (http://moral.wjh.harvard.edu/), recruit thousands of male and female subjects, with educational levels that range from elementary school to graduate degrees, with political affiliations that range from liberal to conservative, and religious backgrounds that range from devout to atheist. In each of these studies, subjects read and judged the moral permissibility of an action on a 7pt-Likert scale [. . .]. Each scenario presented a contrast between a harmful action and a significant benefit in terms of lives saved."

Moral dilemmas come in all shapes and sizes (source here)

The hypothetical scenarios in the test present dilemmas where actions that are evidently harmful to human life considered in isolation result in significant benefits to other humans (whose lives are saved). The generalized results are as follows:

"More specifically, in dozens of dilemmas, and with thousands of subjects, the pattern of moral judgments delivered by subjects with a religious background do not differ from those who are atheists, and even in cases where we find statistically significant differences, the effect sizes are trivial."

This conclusion is the anchor-point for the author's wide-ranging discussion of the origin of morality and, as indicated in their title, the origin of religion. In evaluating their paper, we need to consider whether their empirical starting point is robust enough to carry such far-reaching conclusions.

Some caution is needed in the way "religious background" is understood. There is no systematic probing of the concept in the web-based questionnaire. Participants have to select a label that best fits their current religion, the religion of their upbringing, and locate themselves on the spectrum of "not-at-all" religious to "very" religious. This is all pretty superficial and subjective, given the diversity of religious experience around the world. There is no attempt to use Likert scales to assess the degree to which respondents understood God to be a creator, transcendent, immanent, able to answer prayer or, even more relevant, the reference point for our sense of right and wrong. Consequently, the term "religious" is 1-dimensional and almost devoid of content. Yet, the authors place considerable weight on their analysis of responses gathered.

More caution is needed when we read in the above quote about "trivial" effect sizes. In another study the authors mention, radical altruism was the focus of interest: does religious background affect thinking about whether to sacrifice ones own life "in order to save the lives of a greater number of anonymous others". Significant differences were found. But these could be predicted, say the authors, "given the fact that many religions praise martyrdom". They go on to offer this analysis:

"[A]lthough there are significant evolutionary pressures against such acts of radical altruism, religious pressures might lead people to offer this judgment because they believe it is the morally appropriate answer. What religion can do, and what political and legal institutions can do as well, is alter local and highly specific cases. And yet, they appear to have no influence at all on the intuitive system that operates more generally, and for unfamiliar cases."

These comments about the need for caution are intended to show that the authors have a very inadequate view of the concept of "religion". To them, the various religions can all be lumped together and there are no distinctions worth making. They do not see the need to explain why they think that radical altruism can somehow be linked to the praise of martyrdom. Even when differences are discernable between the moral judgments of the religious and those of atheists, they are considered trivial apparently because there are (untested) evolutionary explanations of why the religious are so minded. All this raises questions about the adopted methodology and the analysis of the authors.

Before making further comments on the arguments built on the empirical findings, it is useful to note some comments by Philip Ball, writing a column for Nature. He draws attention to the conceptual framework underpinning the research: "By taking it as a given that religion is an evolved social behaviour rather than a matter of divine revelation, [the authors' paper] tacitly adopts an atheistic framework." Ball is absolutely right, and we can add the thought that tacit atheism is a pervasive problem in many areas of scholarly activity. Given their presuppositions, no one should expect the authors to reach a conclusion that challenges atheism. However, this does not mean such conclusions cannot be drawn by others who approach the same data with a different conceptual framework.

The first thesis developed in the paper is that "moral intuitions operate independently of religious background" and are therefore not explained by religion. The authors develop an analogy with linguistics, where the concept of innate ability for language acquisition is widely held, and this innate ability is independent of the cultural background. Ball describes this thesis in this way:

"The paper [ . . ] challenges the assertion commonly made in defence of religion: that it inculcates a moral awareness. If we follow the authors' line of thinking, religious people are no more likely to be moral than atheists."

Whenever there is only one hypothesis on the table, there should be concern! Scholars should be cultivating multiple working hypotheses and looking for ways of testing them. To show the significance of an alternative conceptual framework, consider a perspective that understands mankind as made in the image of its Designer. Innate abilities are imparted by this Designer: we speak because the Designer speaks; we have a moral awareness because the Designer is the reference point for what is right and what is wrong. These innate abilities affect all people - whether they are atheists or religious, whether they are pantheists or theists, whether they are male or female, young or old. This is a hypothesis that explains the data and scholars who "tacitly adopt[] an atheistic framework" are excluding this alternative purely on ideological grounds.

The second thesis is concerned with the origin of religion. The authors think their work on moral intuitions leads naturally to the hypothesis that religion is a by-product of pre-existing capabilities.

"Specifically, recent work in moral psychology supports the view that religion evolved as a cognitive by-product of pre-existing capacities that evolved for non-religious functions."
[. . .]
"Religion is a set of ideas that survives in cultural transmission because it effectively parasitizes other evolved cognitive structures."
[. . .]
"Here again, religion stands on the shoulders of cognitive giants, psychological mechanisms that evolved for solving more general problems of social interactions in large, genetically unrelated groups."

For the purposes of this blog, we shall defer comment and let Philip Ball speak: "Whether it [i.e. the research] 'explains' religion is another matter."

"It's debatable, however, whether these moral tests are probing religion or culture as a moral-forming agency, because non-believers in a predominantly religious culture are likely to acquire the moral predispositions of the majority. Western culture, say, has long been shaped by Christian morality. [. . .] But to uncover religion's roots, is morality necessarily the best place to look? It seems hard to credit the idea that the immense cultural investment in religion was made merely to strengthen and fine-tune existing neural circuits related to morality. [. . .] Yet attempting to explain the origins of such a rich cultural phenomenon as religion is doomed to some extent to be a thankless task. For to 'explain' Chartres Cathedral or Bach's Mass in B Minor in terms of non-kin cooperation is obviously to have explained nothing."

The origins of religion: evolved adaptation or by-product?
Ilkka Pyysiainen and Marc Hauser
Trends in Cognitive Sciences, 14(3), 104-109, March 2010 | doi:10.1016/j.tics.2009.12.007

Abstract: Considerable debate has surrounded the question of the origins and evolution of religion. One proposal views religion as an adaptation for cooperation, whereas an alternative proposal views religion as a by-product of evolved, non-religious, cognitive functions. We critically evaluate each approach, explore the link between religion and morality in particular, and argue that recent empirical work in moral psychology provides stronger support for the by-product approach. Specifically, despite differences in religious background, individuals show no difference in the pattern of their moral judgments for unfamiliar moral scenarios. These findings suggest that religion evolved from pre-existing cognitive functions, but that it may then have been subject to selection, creating an adaptively designed system for solving the problem of cooperation.

Morals don't come from God
Philip Ball
Nature, 8 February 2010 | doi:10.1038/news.2010.55

Abstract: The finding that religion scarcely influences moral intuition undermines the idea that a godless society will be immoral, says Philip Ball. Whether it 'explains' religion is another matter.

See also:

Morality Research Sheds Light on the Origins of Religion, ScienceDaily (9 February 2010)

Hunter, C. Important New Paper on Evolutionary Explanation, Darwin's God (8 February 2010)

by Denyse O'Leary
ARN correspondent

When Britain's Guardian newspaper first introduced its "evolutionary agony aunt", this writer thought - a spoof for sure. But where evolutionary psychology is concerned, it can be genuinely hard to tell.

No spoof. The Guardian burbled proudly, "A mere 150 years after Darwin published On the Origin of Species, we are proud to introduce our very own Evolutionary Agony Aunt" in the person of Carole Jahme, author of Beauty and the Beasts: Woman, Ape and Evolution and star of comedy Carole Jahme is Sexually Selected, described as a combination of Charles Darwin and Charlie Chaplin. We were told that her column will shine the "cold light" of evolutionary psychology on readers' problems, in sharp contrast to the glossy magazines.

Carole counsels her troubled readers by citing the behaviour of chimpanzees, other apes, and monkeys. And with what result?

Go here for the rest.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

By Robert Deyes
ARN Correspondent

Santa Fe Institute economist Brian Arthur believed that much of what we see in global economic patterns can be explained by a process of "locking in" of historical events (1). Notably, the success of the QWERTY keyboard or the increased sales of the VHS video system over its arch rival Beta Max did not depend so much on any inherent better quality of the winning system but rather on small details in the history of innovation that, over time, lead to the establishment and the overwhelming success of particular technologies (1). Once such winning technologies became wide-spread, they became a locked and established part of our culture.

Arthur undoubtedly received much of his insight from long conversations that he had with biophysicist Stuart Kaufman as the two of them thrashed out the concepts of biology and economic policy in an attempt to reconcile both under the umbrella of their unifying theory of complexity (1). It was clear that a great number of parallels could be drawn between these two otherwise distinct areas of research.

From an origin of life standpoint, Kauffman has long been unconvinced by the usual crop of prebiotic synthesis experiments. There is after all no basis upon which to suppose that amino acids and nucleotides could randomly form long polymer chains with specific functions such as we see in the cell (2). Following such a realization Kauffman became enthralled by the idea that maybe there was a self-organizing process through which compounds could come together in an autocatalytic cycle- a closed cycle of catalysts that converted one molecule to another in a self sustaining fashion (3). What was interesting about Kauffman's idea was the manner through which he reached it- a multidisciplinary environment, such as the Santa Fe Institute with economists, political analysts and archaeologists coming together to look for a common thread uniting the emergence of complexity in lost civilizations, economically autonomous states and ultimately life's biochemistry.

One of Kauffman's favorite concepts- the 'adjacent possible'- describes a collection of molecules that are not actually in existence within the universe but are nevertheless one reaction step away from being synthesized (4). Thus the adjacent possible always exists since, once new molecules are synthesized, there is a new set of molecules that can always be made from these in a single reaction. Kauffman proposes that, ever since its origin, the earth's biosphere has been expanding into the adjacent possible as new molecules and compounds have become available (4). From a thermodynamic stance, the expansion of the biosphere into the adjacent possible would represent a displacement from equilibrium that, according to Kauffman, would provide the necessary chemical potential for driving the actual state of molecular diversity into the infinite adjacent possible. In other words many diverse molecules would emerge over time amongst which some would have the necessary properties to behave as biological catalysts. Given enough time, anything could happen.

While captivating in simplicity and imaginative content, Kauffman's cogitations on the emergence of life have done precious little to shake off the explanation-critical question of how specificity had arisen within his proposed autocatalytic cycles. The operative units of such cycles, namely proteins and nucleic acids, could not all exhibit low specificity if a self-reproducing metabolic cycle were to be in any way sustainable. Philosopher Stephen Meyer's exegesis on this matter is profoundly relevant. "It does not follow, nor is it the case biochemically" writes Meyer "that just because some enzymes might function with low specificity, that all the catalytic peptides (or enzymes) needed to establish a self-reproducing metabolic cycle could function with similarly low levels of specificity and complexity" (5). As Meyer later adds:

"For the direct autocatalysis of integrated metabolic complexity to occur, a system of catalytic peptide molecules must first achieve a very specific molecular configuration. This requirement is equivalent to saying that the system must start with a large amount of specified information or specified complexity...Self organizational models either failed to solve the problem of the origin of specified information or they "solved" the problem at the expense of introducing other unexplained sources of information. Kauffman's models provided only the best illustration of this latter "displacement problem."" (5)

Kauffman's concept of an infinitely expanding adjacent possible dies an early death when one starts dealing with actual numbers. Consider, for example, the number of possible amino-acid sequences that we can come up with for a protein that is 200 amino acids in length (numbers that are cited by Kauffman himself; 6). Proteins are made up of 20 different amino acids most of which are precisely arranged so as to attain specific functions. This means that for a protein that is 200 amino acids long, there are approximately 20exp200 possible ways that these amino acids can be lined up (ie 10exp260 proteins). Given that the total number of particles in the known universe is estimated to be around 10exp80 and considering Kauffman's own calculation for the total number of reactions since the big bang as being 10exp193, it is easy to see that the universe has not been around for long enough to cover even a small fraction of these 10exp260 proteins (6). In fact, Kauffman posits that it would take 10exp67 times the current age of the universe to cover all possible protein combinations for a protein of this size (6).

We can forget the idea of ever being able to cover the full panoply of amino-acid combinations for a 200 amino-acid long protein. Nevertheless can we find solace in the context of the cell where catalytic events may speed up the rates of reaction and thus cram the adjacent possible into the incredibly short? The answer here is an even flatter no. To understand why, we must visit another of Kauffman's key ideas, that of 'self-organized criticality' (7). When we say that cells are subcritical, what we are really saying is that they have an extremely constrained rate of expansion of molecular diversity- much more constrained than Kauffman's adjacent possible biosphere. If it were much faster, cells would invariably die. We now know that viruses and bacteria are well below this so-called error catastrophe (7).

What does this mean for the exploration of the vast molecular space? Simple- the organization of molecules into a cellular 'living' context does nothing to shorten the time required to find those 200 amino-acid long proteins that are going to perform useful functions. In fact, because of their subcritical state, the search for functional proteins in a cell only becomes more drawn out. Molecular biologists Jean Jacques Toulme and Richard Giege point out how nature just has not had the time to visit the vast extent of combinatorial space that defines the protein world (8). In true neo-Darwinian style, they nevertheless assure us that the current repertoire of proteins could easily have evolved from a selected few precursors (8). If that is not blind faith, I do not know what is.

Further Reading
1. M. Mitchell Waldrop (1992), Complexity, The Emerging Science At The Edge Of Order And Chaos, Simon & Schuster, New York, pp.49
2. ibid p.122
3. ibid p.123
4. Stuart Kauffman (2000), Investigations, Published by Oxford University Press, New York, p.142-144
5. Stephen Meyer (2009) Signature In The Cell: DNA And The Evidence For Intelligent Design, Harper Collins Publishers, New York, p.262
6. ibid, p.142
7. ibid pp.152, 207-209, 216, 244
8. Jean-Jacques Toulme and Richard Giege (1997), Une introduction a la science des aptameres; Atelier de formation INSERM, 'Strategies combinatoires pour la selection d'oligonucleotides a fonction predefinie: applications en biologie'

It is well known that Darwin speculated on what might happen in "some warm little pond" (previously discussed here). But it was not until 1929 that J.B.S. Haldane developed a testable hypothesis involving a "prebiotic broth, or primordial soup". He proposed that organic compounds were made when methane, ammonia and water reacted as a result of energy supplied by ultraviolet radiation. The reaction products were suggested to have accumulated in a "hot dilute soup" in the primeval earth. In this scenario, further reactions led to macromolecules, protocells and then life.

"Backed up by Stanley Miller's (1953) inorganic synthesis of organic molecules in the laboratory, it seemed to generations of scientists that Haldane's narrative was basically right, and all that was left was to sort out the details."

It is time to move on from this unproductive research (source here)

Miller's experiments became an icon of naturalistic evolution and entered the textbooks with very little critical analysis of the findings. Even recently, Miller's work was acclaimed in the journal Science. Happily, there are opportunities to get beyond the hype but, as Jonathan Wells showed in his Icons of Evolution, these contributions rarely get beyond the technical literature. William Martin and colleagues have presented a strong case for retiring the primordial soup concept from active service. It has reached the grand old age of 81 and, as a hypothesis, it has not been confirmed. Normally, when hypotheses are tested and found wanting, they are discarded - but we are now overdue for this to happen with the primordial soup. It is "well past its sell-by date".

Two reasons are provided in the paper. The first is that a soup of organic chemicals will be in thermodynamic equilibrium. The reaction products are already present and there is no obvious source of energy to drive polymerisation or any other significant change. "Ionizing UV radiation inherently destroys as much as it creates."

"[T]he homogeneous soup has no internal free energy that would allow them to react further. Life is not just about replication; it is also a coupling of chemical reactions - exergonic ones that release energy and endergonic ones that utilise it, preventing the dissipation of energy as heat. It is commonplace to say that life requires energy, but the conception of a primordial soup fails to recognise or incorporate the importance of energy flux. On the congruence principle, what life needed was not some harsh and problematic source of energy like UV radiation (or lightning), but a continuous and replenishing source of chemical energy."

The second reason concerns fermentation as the primordial mechanism of energy generation in a world without oxygen. Haldane promoted this idea, and De Duve supported it as the mechanism for sustaining anaerobic life. "If there can be said to be a textbook view, this is it."

"But there are profound difficulties - both chemical and biological - in viewing fermentation as primitive rather than derived. Fermentation is chemically a disproportionation - not a simple redox reaction, in which electrons are stripped from a donor and passed onto an acceptor, driven by strong thermodynamics. In contrast with respiration, the amount of energy released by fermentation is tiny, reflecting its lack of thermodynamic driving force. To tap such an insignificant source of energy requires more rather than less sophistication, and indeed about 12 enzymes are needed to catalyse a complex succession of steps in glycolytic-type fermentations based around the Embden-Meyerhoff pathway. These enzymes are proteins encoded by genes, which would have had to evolve as a functional unit without any other source of energy in the primordial oceans - close to an impossibility in an RNA world, let alone the only way to evolve one."

The authors go on to defend their view that fermentation is a sophisticated, rather than a primordial, derivation. This brings them to the crunch question:

"But if there was no soup, and no energy from UV radiation or fermentation, then where was the energy that powered the emergence of life?"

They go on to propose alkaline hydrothermal vents as the primordial source of energy for life. They develop their idea that the origin of life can be considered distintly from the origin of replication. They support Russell et al's (1993) proposal that chemiosmosis is "an inherent property of life, one inherited from the very place and space where it arose". Their paper is exploratory, not plotting out any details of what the Last Universal Common Ancestor (LUCA) looked like, but considering how chemiosmosis might have worked in the setting of alkaline hydrothermal vents. Further discussion of this is needed, of course, but this blog is to draw attention to the challenge these authors present to OOL researchers generally and to textbook authors/educators.

"It is time to cast off the shackles of fermentation in some primordial soup as 'life without oxygen' - an idea that dates back to a time before anybody had any understanding of how ATP is made - and to embrace the most revolutionary idea in biology since Darwin as the key not only to the bioenergetics of all life on Earth today, but to its very origin.(80) Thus it seems to us likely that LUCA grew on the H2/CO2 couple, and that she was naturally chemiosmotic."

How did LUCA make a living? Chemiosmosis in the origin of life
Nick Lane, John F. Allen, William Martin
Bioessays, Published Online: Jan 27 2010 | DOI: 10.1002/bies.200900131

Despite thermodynamic, bioenergetic and phylogenetic failings, the 81-year-old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup is homogeneous in pH and redox potential, and so has no capacity for energy coupling by chemiosmosis. Thermodynamic constraints make chemiosmosis strictly necessary for carbon and energy metabolism in all free-living chemotrophs, and presumably the first free-living cells too. Proton gradients form naturally at alkaline hydrothermal vents and are viewed as central to the origin of life. Here we consider how the earliest cells might have harnessed a geochemically created proton-motive force and then learned to make their own, a transition that was necessary for their escape from the vents. Synthesis of ATP by chemiosmosis today involves generation of an ion gradient by means of vectorial electron transfer from a donor to an acceptor. We argue that the first donor was hydrogen and the first acceptor CO2.

See also:

New Research Rejects 80-Year Theory of 'Primordial Soup' as the Origin of Life, ScienceDaily (3 February 2010)

Warren, D. Back to the beginning, The Ottawa Citizen (6 February 2010)

The Israeli Education Ministry's chief scientist sparked a furor among environmental activists and scholars with remarks questioning the reliability of evolution and global warming theory. The comments from Dr. Gavriel Avital, the latest in a series of written and oral statements casting doubts on the fundamental tenets of modern science, led several environmentalists to call for his dismissal.

"If textbooks state explicitly that human beings' origins are to be found with monkeys, I would want students to pursue and grapple with other opinions. There are many people who don't believe the evolutionary account is correct," Avital said.

More...

There will be a showing of "Darwin's Dilemma" and a dessert, sponsored by Probe Ministries in the Dallas/Fort Worth area on Tuesday, February 23rd.

Details at this Web page

by Denyse O'Leary
ARN correspondent

Here's the reason I asked why human evolution should be taught in school:

I just came across this fact: Human evolution: Little is known other than basic outline

Contrary to widely heard huffing, there are huge gaps in our understanding of early humans. In Nature's 2020 Visions (7 January 2010) Scroll down to Leslie C. Aiello, and we learn

Most of the recent effort in hominin palaeontology has been focused on Africa and Europe. But the announcement in 2004 of the small hominin Homo floresiensis in Indonesia was a warning that we are naive to assume we know more than the basic outline of human evolutionary history. ... Go here for more.

Sorry to be so long judging this one, but there were 143 posts and I had several local issues to deal with at the same time. Now, to business: The winner is Collin at 8. His succinct entry appears below. I would also have awarded a prize to EvilSnack at 48, for this entry, but I only received one copy of David Berlinski's The Deniable Darwin. I will see if I can procure another copy, but if not EvilSnack may contact me anyway. I have other prizes on my shelf.

Winners need to be in touch with me at oleary@sympatico.ca, with a valid postal address. Their names will not be added to a mailing list. There is no mailing list.

Here's Collin:

Human evolution ought to be taught in schools because it is one of the best cases for common descent. This is probably a result of the extra interest among scientists concerning human evolution.

Even creationists and students sympathetic to ID ought to be taught the best argument for Darwinism so that if they want to argue against it they do so against the best scenario the opposition has to offer. Otherwise, those supportive of traditional Darwinism will sense a straw man argument and end up being inoculated against further, more refined and honest arguments.

Some careless creationists in the '80s made this mistake causing further, more compelling arguments to be dismissed before being further evaluated.

Human evolution, being taught, does inform students of a lot of ideas that are not necessarily against ID or even creationism. Presumably even creationists (most of them) will concede that homo erectus did exist as some kind of now-extinct species. Students can be presented with the fact of the bones (or lack thereof) and they can make their own conclusions. My hope is that teachers will present evolution's best arguments but not endeavor to indoctrinate students. Maybe that is a fine line, but it can be done, and is the honest way to go about it.

What swayed me was Collin's emphasis on hearing both sides honestly represented by their own advocates. If schools do not teach students to evaluate on that basis, they are not worth the money we spend on them.

Consider a simple example: Most days, I ride the Toronto Transit System, which features a vast array of busboard ads and subway posters advocating every cell phone offer imaginable. You can be sure that the sales person will not emphasize strongly to the customer, "Our offer is the cheapest - but, of course, we do sign you up for three years, and it costs you $300 to cancel."

The salesperson's competitor does that. The competitor shouts from busboards, subway posters, and billboards, "No contract, no cancellation fee!" That sets the customer thinking about what to ask next time, doesn't it?

Cell phones are a minor matter, of course. But later in life, the student will deal with job offers, marriage proposals, mortgage offers, investment advice, medical plans .... The advocate's offer can only be evaluated by hearing alternatives, clearly spelled out.

One of my major objections to "Darwinism-only" biology education is that - apart from the fact that I don't think it is true - it is not a good way to teach.

Other comments follow:

Read more!

"I would never have predicted that an atheist would name a book about intelligent design as one of the top books of 2009, while another atheist would write a book defending intelligent design?" commented Dennis Wagner, ARN Executive Director, about the organization's Top Ten Darwin and Design Resource List for 2009. "This is a sign that open minds in the academic and scientific communities are beginning to take the evidence for intelligent design seriously," Wagner concluded. He was referring to the number one book on the list, Signature in the Cell: DNA and the Evidence for Intelligent Design by Stephen Meyer and number three book Seeking God in Science: An Atheist Defends Intelligent Design by Bradley Monton.

Kevin Wirth, ARN Director of Media Relations, pointed out that several other resources on the 2009 list show a growing international interest in intelligent design: "Hungarian scientists published an English version of their book, Nature's IQ, that documents over 100 irreducibly complex behaviors in nature, while a well-published British medical doctor documented his reservations about Darwinian evolution in the book Why Us? How Science Rediscovered the Mystery of Ourselves."

An online version of the ARN Top 10 Darwin and Design stories for 2009 with hyperlinks to original news sources can be found at www.arn.org/top10.

"If you don't think viewpoint discrimination is alive and well in this country when it comes to Darwin's theory, then you must be living on another planet," said Dennis Wagner, announcing this year's Top Ten in Media News in the growing Darwin vs. design controversy. This year, top honors went to Texas and Louisiana for protecting students' and teachers' rights to examine and critique all sides of evolution and other controversial science issues.

"The theory of evolution has been elevated to the status of a sacred dogma in many parts of our modern culture" observed Dennis Wagner, ARN Executive Director. "Students, teachers and science professionals have suffered recrimination for challenging Darwin's theory, and political policies like those recently passed in Texas and Louisiana are now required to maintain academic freedom and freedom of speech. Critical thinking skills are key not only to the learning process, but more importantly to scientific progress," said Wagner.

Kevin Wirth, ARN Director of Media Relations, pointed out that several other stories on the 2009 Top Ten Media list indicate the growing need for this type of legislative protection: "Ben Stein was 'expelled' as the commencement speaker at the University of Vermont, Michael Behe was temporarily 'expelled' from Bloggingheads.tv, and the California Science Center censored the showing of a movie that was critical of Darwin’s theory. We thoroughly documented case after case of this type of viewpoint discrimination in the book Slaughter of the Dissidents and the list just keeps on growing."

An online version of the ARN Top 10 Darwin and Design stories for 2009 with hyperlinks to original news sources can be found at www.arn.org/top10.

Two years ago, "the most primitive bat known" was reported in Nature. It was not primitive in its wings and body, but "the morphology of the ear region suggests that it could not echolocate, making it a possible intermediate link between bats and their non-flying, non-echolocating mammalian ancestors". At the time, the find was suggested to settle the question as to which came first: flight or echolocation? The answer was a definite flight first.

"The problem of understanding bat evolution dates back at least to Charles Darwin, who in The Origin of Species enumerated a list of difficulties he saw with the theory of evolution by natural selection. The example often discussed is the origin of the eye. But Darwin also mentioned the vexed issue of how bats had arisen from terrestrial ancestors." Speakman 2008).

Onychonycteris finneyi was featured on the cover of Nature in February 2008 (Source here)

This assessment of the fossil must now be reappraised. New work on modern-day bats has revealed another mechanism of echolocation. One of the authors described the work thus:

"We borrowed 35 specimens from the Royal Ontario Museum in Toronto and performed micro-computed tomography on them. This imaging technique allowed us to see the fine details of the bats' ear and throat regions: the larynges, stylohyals and tympanic bones. Previous work had relied on dissecting these bones, a challenge in animals as small as bats. We found that the fusion or connection of two bone structures - the stylohyal bone in a bat's throat and the tympanic bone in the ear region of its skull - was a feature of all laryngeally echolocating bat species we studied."

This finding is new and unexpected. It means that previous conclusions need to be reappraised. This is exactly what is happening with the "most primitive fossil bat".

"The relatively small cochleae and lack of paddle-like expansions on the cranial tips of the stylohyal bones have been interpreted as evidence that O. finneyi lacked laryngeal echolocation, which supports the hypothesis that flight evolved before echolocation. However, we find that articulation between the stylohyal and tympanic bones is a better predictor of laryngeal echolocation ability than the shape of the stylohyal bone, at least among extant bats. If the stylohyal bones articulated with the tympanic bones in O. finneyi, then we propose that this species had the capacity for laryngeal echolocation. Our results thus reopen basic questions about the timing of the appearance of echolocation and flight in the evolution of bats."

There are several lessons to be learned here - and one of these is to always be prepared to hold judgment on the word "primitive" - even if it is said to be the "most primitive"!

A bony connection signals laryngeal echolocation in bats
Nina Veselka, David D. McErlain, David W. Holdsworth, Judith L. Eger, Rethy K. Chhem, Matthew J. Mason, Kirsty L. Brain, Paul A. Faure & M. Brock Fenton
Nature 463, 939-942 (18 February 2010) | doi:10.1038/nature08737

Echolocation is usually associated with bats. Many echolocating bats produce signals in the larynx, but a few species produce tongue clicks. Here, studies show that in all bats that use larynx-generated clicks, the stylohyal bone is connected to the tympanic bone. Study of the stylohyal and tympanic bones of a primitive fossil bat indicates that this species may have been able to echolocate, despite previous evidence to the contrary, raising the question of when and how echolocation evolved in bats.

Last year, a workshop was hosted by the International Society of Protistologists at their North American Section Meeting. The workshop was given the title "Horizontal Gene Transfer and Phylogenetic Evolution Debunk Intelligent Design". Some of the presentations have recently been published, and one of these is the focus of attention here. One does not get beyond the first paragraph before finding that the authors regard Neodarwinism as robust and that all challengers have abandoned science:

"Despite the overwhelming body of evidence that supports the basic tenets of evolution (i.e. common descent of organisms with different forms being the result of natural selection acting upon naturally occurring variation), there is a large proportion of the American population that does not accept the validity of what is perhaps the most rigorously tested scientific hypothesis in history."

The "six" kingdom taxonomic scheme (Image from Purves et al., source here)

The second paragraph points the finger at Dr Michael Behe and his influential books Darwin's Black Box and The Edge of Evolution. Although the paper covers much ground, it is one of Behe's arguments that engage their attention.

"In his book "The Edge of Evolution: The Search for the Limits of Darwinism" Behe (2007) draws heavily upon the example of drug resistance in the malarial parasite Plasmodium falciparum as one biochemical pathway that is supposedly too complex to have arisen through natural evolutionary processes. According to Behe (2007), the odds that mutations required to impart chloroquine resistance in Plasmodium could arise naturally are so impossibly long that they lie beyond what he considers "The Edge of Evolution".

Anyone who has read Behe's book and understands his analysis would be alerted at this point to a wearying straw man argument. If you are going to critique someone, you ought to, at least, be able to paraphrase their arguments correctly. One wonders why the workshop participants did not put the authors right. In addition, one wonders why the referees did not point out the need for correction. But further, one wonders why the journal editor did not invite peer review from an ID microbiologist. Certainly, the peer review system failed on this occasion. Happily, the internet does allow misinformation to be corrected, and Behe has posted comments which show that the authors, instead of "dispelling the myths of Intelligent Design" are actually promoting myths about Intelligent Design. Here are Behe's concluding words:

"To recap, several years after The Edge of Evolution was published a scientific society held a workshop to demonstrate the book's errors. Yet they couldn't even get the book's argument straight, and the experimental work they cited against my argument is not even pertinent to it. Apparently the design argument drives some scientists so much to distraction that they lose their normally robust powers of reasoning."

Clearly, there is more to be said about the underlying issues. In the abstract of the paper, ID advocates are said to have the goal of "challenging the philosophy of scientific materialism". This is a good place to start an analysis of the issues: because scientific materialism needs to be challenged. Science has no basis for concluding that matter is all there is and that all causation is natural. Those who claim this are importing an ideology that was absent in the early days of science (when the pioneers were theistic scientists, who were quite comfortable with the thought that the natural world is designed). People with different ideologies look at the same data in different ways, and protagonists who do not recognise this are spreading more heat than light. My fear is that instead of discarding this paper as based on false premises, blind crusaders for philosophical materialism will hail it as "excellent article" and will add it to their list of peer reviewed publications showing that the ID approach is bankrupt.

Using Protistan Examples to Dispel the Myths of Intelligent Design
Mark A. Farmer and Andrea Habura
Journal of Eukaryotic Microbiology, 57(1), 2010, 3-10 | doi 10.1111/j.1550-7408.2009.00460.x

ABSTRACT: In recent years the teaching of the religiously based philosophy of intelligent design (ID) has been proposed as an alternative to modern evolutionary theory. Advocates of ID are largely motivated by their opposition to naturalistic explanations of biological diversity, in accordance with their goal of challenging the philosophy of scientific materialism. Intelligent design has been embraced by a wide variety of creationists who promote highly questionable claims that purport to show the inadequacy of evolutionary theory, which they consider to be a threat to a theistic worldview. We find that examples from protistan biology are well suited for providing evidence of many key evolutionary concepts, and have often been misrepresented or roundly ignored by ID advocates. These include examples of adaptations and radiations that are said to be statistically impossible, as well as examples of speciation both in the laboratory and as documented in the fossil record. Because many biologists may not be familiar with the richness of the protist evolution dataset or with ID-based criticisms of evolution, we provide examples of current ID arguments and specific protistan counter-examples.

Misusing Protistan Examples to Propagate Myths about Intelligent Design
Michael J. Behe
Uncommon Descent, 15 February 2010

Introductory sentences: The Journal of Eukaryotic Microbiology recently published several papers from a workshop sponsored by the International Society of Protistologists entitled "Horizontal Gene Transfer and Phylogenetic Evolution Debunk Intelligent Design." So here we have a respected scientific society, presumably planning a workshop months in advance, and finally laying out their considered case for why intelligent design fails. As you might imagine, I was most anxious to read about it. Unfortunately, rather than scholarly papers, the manuscripts read like press releases from the National Center for (Darwinian) Science Education.

By Robert Deyes
ARN Correspondent

2010 sees the beginning of a new series in Spanish exploring key findings from contemporary science that support the intelligent design inference. The series Paseos Por La Naturaleza (A Walk Through Nature) aims to further strengthen the global influence that the Intelligent Design movement already enjoys and raise awareness of important academic resources that are today challenging orthodox Darwinism and revitalizing the call for a fresh perspective on scientific discourse.
Second installment can be found at:

Paseos Por La Naturaleza

OIACDI

(transl: New Intelligent Design Book A Landmark Assault On Scientific Naturalism)

Much to the dismay of the BADs (Birds Are Dinosaurs), there is a group of scientists who are in denial of the thesis that theropod dinosaurs evolved into birds. Furthermore, this BAND of scholars (Birds Are Not Dinosaurs) have published in the esteemed PNAS and not in some obscure low-ranked journal. The research was concerned with the dromaeosaurid Microraptor gui, which was first described in 2002 and has flight feathers on all four limbs. The research team modelled M. gui flight and concluded that gliding was its forte.

"We suggest that Microraptor was an adept glider and would have had little difficulty gliding from tree trunk to tree trunk or climbing trees, but would have been very awkward and vulnerable on the ground. The primary feathers on the tarsometatarsus (foot) of the hindwing of M. gui were too long in relation to the limb bones to have allowed the hindwing to fold compactly as does the modern bird wing. Just as colugos and sloths have their limbs encumbered by patagia, the hindwing feathers on Microraptor would severely hamper any terrestrial locomotion."

John Ruben draws attention to an image drawn in 1915 by naturalist William Beebe. It suggests a hypothetical view of what early birds may have looked like, gliding down from trees - and it bears a striking similarity to a fossil discovered in 2003 that is raising new doubts about whether birds descended from ground-dwelling theropod dinosaurs (Source here)

In an accompanying commentary, John Ruben reviewed the history of the controversy over the origins of bird flight. Much to the disapproval of the BADs, Ruben presents those skeptical of the cursorial, ground-upwards hypothesis as scholars who have championed reasoning from evidence. The new research, Ruben suggests, favours gliding, arboreal proto-birds. But he also suggests that some more radical thinking may be warranted:

"So, is the answer, after all, a hybrid of the two old theories, i.e., avian origins from an arboreal, gliding theropod dinosaur? Perhaps, but then this is paleobiology - very recent data suggest that many clearly cursorial theropods previously thought to have been feathered may not have been so and that dromaeosaurs, the group that birds are assumed to have been derived from, may not even have been dinosaurs. What pops up next is anyone's guess."

The Science Daily report points to these more fundamental divergences of view:

The weight of the evidence is now suggesting that not only did birds not descend from dinosaurs, Ruben said, but that some species now believed to be dinosaurs may have descended from birds.
"We're finally breaking out of the conventional wisdom of the last 20 years, which insisted that birds evolved from dinosaurs and that the debate is all over and done with," Ruben said. "This issue isn't resolved at all. There are just too many inconsistencies with the idea that birds had dinosaur ancestors, and this newest study adds to that."

Breaking out of the conventional wisdom? Yes - we need some more of that!

Paleobiology and the origins of avian flight
John Ruben
Proceedings of the National Academy of Sciences, published online before print February 9, 2010 | doi:10.1073/pnas.0915099107

First sentence: Interpreting the paleobiology of long extinct taxa, pesky new fossils, and reinterpretations of well-known fossils, sharply at odds with conventional wisdom never seem to cease popping up.

Model tests of gliding with different hindwing configurations in the four-winged dromaeosaurid Microraptor gui
David E. Alexander, Enpu Gong, Larry D. Martin, David A. Burnham, and Amanda R. Falk
Proceedings of the National Academy of Sciences, Published online before print January 25, 2010 | doi: 10.1073/pnas.0911852107

Abstract: Fossils of the remarkable dromaeosaurid Microraptor gui and relatives clearly show well-developed flight feathers on the hind limbs as well as the front limbs. No modern vertebrate has hind limbs functioning as independent, fully developed wings; so, lacking a living example, little agreement exists on the functional morphology or likely flight configuration of the hindwing. Using a detailed reconstruction based on the actual skeleton of one individual, cast in the round, we developed light-weight, three-dimensional physical models and performed glide tests with anatomically reasonable hindwing configurations. Models were tested with hindwings abducted and extended laterally, as well as with a previously described biplane configuration. [. . .] Although the biplane model glided almost as well as the other models, it was structurally deficient and required an unlikely weight distribution (very heavy head) for stable gliding. Our model with laterally abducted hindwings represents a biologically and aerodynamically reasonable configuration for this four-winged gliding animal. M. gui's feathered hindwings, although effective for gliding, would have seriously hampered terrestrial locomotion.

See also:

Bird-from-Dinosaur Theory of Evolution Challenged: Was It the Other Way Around?, ScienceDaily (Feb. 10, 2010)

Deyes, R. B.A.R.B: Birds Are Really.....Birds!, ARN Literature Blog (25 June 2009)

Tyler, D. Did birds fly in the Late Triassic? ARN Literature Blog (16 June 2009)

Synopsis Of Chapter Eleven, Signature In The Cell by Stephen Meyer
ISBN: 9780061894206; ISBN10: 0061894206; Imprint: HarperOne

By Robert Deyes
ARN Correspondent

Biological determinists will argue on the assumption that universal laws undergird the origin of life. Such an appeal to natural law is of course not a novel one. Indeed even thousands of years ago Aristotle philosophized over the existence of some universal organizing principle that could shape life into the easily identifiable forms we see today. From a protein sequence perspective Pennsylvania State University biochemists Gary Steinman and Marian Cole gave seemingly empirical substance to the idea that there were certain combinations of amino acids that were more likely to form as a direct result of amino-acid bonding energies.

Along the same grain, biophysicist Dean Kenyon became a die-hard advocate of the view that proteins first assembled into functional entities through the selective affinities that specific amino acids had for one another. To be sure, Kenyon believed that specific protein sequences were somehow predestined to form as a direct result of such constraints. The title of his much-respected tome Biochemical Predestination, which he co-authored with Steinman, became a spark that served to boost his credibility. But as his joint book garnered strength as a staple text for biochemistry graduate studies in the 1970s, Kenyon himself began to have personal doubts over the validity of his own proposition. Interviewed as part of the Discovery Institute's documentary Unlocking the Mystery Of Life, Kenyon's own testimonial brought clarity to the depth of his ongoing struggles:

"There was this enormous problem of how you could get together into one tiny sub-microscopic volume of the primitive ocean all of the hundreds of different molecular components you would need in order for a cell replicative cycle to be established. And so my doubts into whether amino acids could order themselves into meaningful biological sequences on their own without pre-existing genetic material being present just reached an intellectual breaking point. The more I conducted my own studies including a period of time at the NASA Ames Research Center the more it became apparent that there were multiple difficulties with the chemical evolution account".

I first learned of Kenyon's misgivings in the Foreword he wrote for another ground-shifting manifesto The Mystery Of Life's Origins where he noted how it was the information-bearing attributes of both polynucleotide and polypeptide sequences that he had found most vexing and unexplainable. For Stephen Meyer, his own philosophical pilgrimage brought him to the writings of Michael Polanyi who at the end of the 1960s argued that the language-style content of DNA could not be reduced to the mere operation of natural and physical laws. Just as the ink on a paper could not explain the message communicated on a printed page, so the information conveyed in a DNA molecule transcended the chemical and physical properties of its smaller component subunits.

The structures of DNA and RNA presented no escape chute for the chemical evolutionist. As with proteins, there were no constraining forces or 'differential affinities', this time along the phosphate backbones of DNA and RNA, that would make any given base sequence more likely than any other. Meyer transpicuously relays this point to the reader by comparing the base letters of DNA and RNA to magnetic letters on the metallic surface of a refrigerator (For further discussion see We Have No Excuse: A Scientific Case for Relating Life to Mind by Robert Deyes and John Calvert). In the same way that the placing of such letters into meaningful strings cannot be reduced to the magnetic forces between them and the refrigerator, so the information-carrying aspects we observe in DNA and RNA bases cannot be attributed to physical and/or chemical constraints.

Constructing his case on the shoulders of prominent philosophers and scientists, Meyer shows how the absence of biological determinacy is a fundamental feature of both codon/amino-acid assignments and the correspondence between amino acids and their respective tRNA molecules. The need for sequence "freedom" in DNA is imperative if it is to be a molecule of "virtually unlimited novelty" that can store information. To draw yet again from one of Meyer's outstanding depictions, there is no more inevitability in the assembly of functional genes from the ground up than there is in the construction of the palace of Versailles from bricks and mortar.

by Denyse O'Leary
ARN correspondent

A while back, I wrote about a self-absorbed female Darwinist* who was misshelving Mike Behe's Edge of Evolution in the "religion" section of the bookstore, to make some odd personal point:

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

Discovery Institute has two intensive summer seminars on intelligent design, science, and culture from July 9-17, 2010 in Seattle. The first seminar is for students in the natural sciences and philosophy of science; the second seminar is for students in the social sciences and humanities (including politics, law, journalism, and theology).

These seminars are designed for highly-motivated college students who seek a deeper understanding of science and its implications for society. The seminar focusing on ID in the natural sciences will explore the scientific issues in greater technical detail and the seminar on ID in the social sciences and humanities will give more in-depth attention to the social impact of science. This year's seminar will feature Michael Behe, Douglas Axe, Stephen Meyer, Jay Richards, and many other leading lights in the intelligent design community.

Discovery Institute will pay expenses for students who are accepted into this special program (travel, lodging, meals, books and other course materials). Applications will be accepted until April 16, 2010.

More...

by Denyse O'Leary
ARN correspondent

Listen to these, and don't have a fight with someone on your cell phone while driving:

1.

Moving the Goalpost: How Darwin's Theory Survives

It's easy to win the game when you can move the goalpost.

On this episode of ID the Future, biologist and Discovery Institute Senior Fellow Jonathan Wells explains how Darwinism, unlike football, has only one rule: survival of the fittest. The fittest are those who survive, and Darwinists are determined to survive at all costs—even if it means moving the goalpost.

Go here to listen.

(Note: This one is quite interesting because Wells talks about how his observation that a specific type of speciation needed by Darwinism has not been observed was recently distorted in a science mag to say that speciation - as such - has never been observed. This tells me that the commitment of many scientists to Darwinism is not to the idea of speciation as such, but to a broader philosophical commitment to a method by which it must happen, a method that supports broader philosophical ideas. Remember that 78% of evolutionary biologists are pure naturalists - no God and no free will.)

2.

Is the Cell Like a Computer?

On this episode of ID the Future, Casey Luskin interviews Dr. Donald Johnson, author of Probability's Nature and Nature's Probability: A Call to Scientific Integrity. As both a chemist and a computer scientist, Dr. Johnson explains how the cell uses programming code, much like a computer, and he elucidates how the information is processed and converted from proteins into DNA. Listen in as Dr. Johnson shares the science of how the cell is like a computer.

Donald E. Johnson holds PhDs in Computer & Information Sciences from the University of Minnesota and in Chemistry from Michigan State University. He can be reached at his website,ScienceIntegrity.net.

Go here to listen.

(Note: In two important way, cells are not like computers. When my machine is bust, it is just bust, and my local nerd must visit. If I need a new one, it must be bought and unpacked, and inevitably, I will need him back again as something is sure to go wrong. Millions of cells die every day and are replaced, with no loss of function. Fancy that, computer!)

3.

Alfred Russel Wallace: Champion of Natural Selection or Intelligent Design?

On this episode of ID the Future, CSC's Robert Crowther takes a look at Alfred Russel Wallace, who, along with Darwin, co-presented the theory of natural selection in letters to the Linnean Society of London over 150 years ago. Contrary to Darwin, Wallace actually believed that it was possible to detect design in nature. What would modern Darwin defenders make of Wallace today? Listen in and find out.

Go here to listen.

(Note: Actually, they have been doing a number on Wallace for centuries, as Mike Flannery points out. Go here or here for an example. Wallace, with thought design played a role in evolution, was just not as useful for propaganda purposes and was of a much lower social class than Darwin. Here is somewhat from my review of Flannery's book.)

4.

Deepening Darwin's Dilemma With Jonathan Wells

This episode of ID the Future features biologist and Discovery Institute Senior Fellow Jonathan Wells, who explains why Darwin saw the Cambrian explosion as a serious argument against his theory. Darwin countered it by supposing that fossils of the ancestors of Cambrian animals once existed, but were destroyed.

Listen in and learn how the discovery of microscopic and soft-bodied Precambrian fossils makes Darwin’s excuse sound hollow.

Go here to listen.

(Note: It gets better. The Smithsonian sat on the Cambrian fossils for decades because they did not support Darwin's theory. Yes, yes, that Smithsonian, currently alleged to have pressured California Science Center into cancelling a Cambrian film that - I gather - raises the Cambrian problem. [Almost all modern phyla of life forms appeared rather suddenly about 550 million years ago. This is just not the story Darwin was telling and he knew it and so did his supporters, and now so do more and more people.])

Any chance all those dusty drawers in the Smithsonian's cellar will be seized as evidence? Maybe we could learn something, and not about the current functionaries' e-mails.

Free advice to the public in general, not to anyone in particular: Do NOT feed bones to the shredder. Nor paper clips. Never feed anything but paper to the shredder, and feed paper with staples only if the firm warrants that the shredder will accept staples.]

5.

"A Matter of Dismal Wet Plops": Stephen Meyer Interviews David Berlinski on Darwinism

This episode of ID the Future features a clip from the recent "Signature in the Cell" event in Tampa, FL, featuring Stephen Meyer, Michael Medved, David Berlinski and Tom Woodward. Listen in as Dr. Meyer interviews Dr. Berlinski about the questions that led him to criticize Darwinism.

Go here to listen.

(Note: Besides being brilliant, Berlinski, a mathematician, is as funny as heck - not always a common combination. We are all familiar, I suppose, with the genius who doesn't get a joke. Well, that's not him, as the title of this pod suggests. I had a lot of fun reading his Devil's Delusion, a shot at publicly funded nonsense in science, of which many people are getting royally tired. Science advisor to Marie Antoinette, check your e-mail.

Never forget: Most people fund science because they think it will help find cures for cancer or get one's country a Nobel Prize in physics [and ain't we proud!] or offer one's kid a stable, respectable job wearing a lab coat. So take that away - make science mean folly about Stone Age Man, exposed e-mail plots, court cases about broken contracts, reasonable doubts subjected to inquisition and persecution - and what happens?

One thing that might very well happen is that people who used to just sigh and pay the bill might start thinking differently. As in ... we've got the headache already, Now, where is the payload?)

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

Professor Steve Fuller is known as a prolific author whose analysis of the scientific enterprise is iconoclastic. He was famously involved as a defense witness in the Kitzmiller v. Dover Area School District (2005) trial, for which he has received a great deal of flak. The essay cited below provides an explanation of his involvement and a challenge for other qualified people to ensure that their voices are heard.

"I believe that tenured historians, philosophers, and sociologists of science - when presented with the opportunity - have a professional obligation to get involved in public controversies over what should count as science. I stress 'tenured' because the involved academics need to be materially protected from the consequences of their involvement, given the amount of misrepresentation and abuse that is likely to follow, whatever position they take."

Why are so few willing to follow this advice? (Source here)

Those who want to read specific comments on the trial should read the essay. My interest here is in the broader issue of what science studies brings to the discussion of origins. Fuller is dissatisfied with the limited scope of the discourse to date because the dominant voices have functioned as "underlaborer[s] to science". He points out "two types of public exemplars" that have been associated with science studies:

"On the one hand, there is the Michael Ruse figure who supplies a historical and philosophical hinterland to the dominant scientific paradigm so as to complement its purely empirical success with a broader cultural and conceptual grounding that will appeal to those unfamiliar with the technical science. On the other hand, there is the Robert Pennock figure, more typical of the younger generation, who outright collaborates with established scientists in their research, providing a running legitimizing narrative in co-authored articles published in technical and popular forums. In both cases, the science studies scholar functions as an underlaborer to science, as opposed to a true metascientist."

Science studies need to rise above partisanship and develop robust contributions to knowledge that do not need the endorsement of the 'scientific consensus' to justify their validity.

"A metascientist evaluates science from a standpoint that does not presuppose the legitimacy of the dominant paradigm. He or she starts by asking why we pursue science in the first place - the question of ends - and then turns to consider the extent to which the normal pursuit of science satisfies those ends. This is the role I have tried to exemplify. [. . .] The approach is 'constructivist' without being 'relativist' in the way these two terms are normally understood in epistemology."

These social epistemological principles are then applied to the origins controversy. Fuller is interested in this debate because it presents so many important and interesting issues needing rational discussion. However, Fuller finds that far too much bigotry has been expressed and has concluded that something needs to be done to raise the level of debate.

"In terms of the evolution-creation controversy, the bottom line for me, then, is not to satisfy the wishes of particular communities by allowing creationism to be taught, but to avoid the opportunity costs to everyone if creationism is not allowed to be taught."

These opportunity costs are worthy of elaboration. Fuller identifies several of these. The first draws attention to the history of science and the fact that many scientists have done good work motivated by the presupposition that the natural world is the handiwork of an Intelligent Designer. Those who say that toleration of ID will be the death of science and the beginning of a new dark age are in denial of history.

"Here I have in mind the overwhelmingly positive role that belief in an intelligent designer has played in motivating religious people to enter and stick with scientific careers, which have resulted in findings that command the assent of even those who lack faith."

The second opportunity cost is academic freedom. Fuller has already made it clear that he thinks tenured academics should be taking the lead in challenging the dominant paradigm. It is simply too risky for others to stick their heads above the parapet - they are easy targets and they get hurt. They are treated as guilty by association and their ideas are deemed unworthy of any further consideration.

"When we start to judge ideas rather than texts, intentions rather than practices, we become complicit in the erosion of academic freedom. Perhaps the most widely publicized recent case to cross that line was the forced resignation of Michael Reiss as director of science education for the Royal Society. Reiss had the temerity to suggest that science teachers should take seriously - albeit critically - creationist queries raised by their students. Reiss, who also holds a chair at the University of London's Institute of Education, based this judgment on his own research on science pedagogy. It is worth noting that he did not propose that teachers should themselves introduce the creationist ideas - yet the Royal Society deemed he still had to go."

The third opportunity cost is concerned with the quality of debate. Academics are supposed to use their minds when defending a position or critiquing others. However, the origins issue reveals people ruled by emotions, prejudices and ideologies.

"The pervasive anti-Christian bigotry surrounding the evolution-creation debate has had other knock-on effects on the conduct of intellectual discourse. It becomes an excuse to lower the tone in both academic and public discussions. Anyone prepared to defend any form of creationism should expect enormous negative attention in the blogosphere, ranging from occasional derision to outright invitations to trash the defender. At first I believed that my own intervention would clarify misunderstandings but it only seemed to intensify them, not least because I addressed my opponents in the spirit they addressed me. They were not prepared to entertain the idea that it was they and not I who misunderstood."

These three opportunity costs deserve the serious attention of all who are engaged in the controversy. However, the dominant response has been to ignore these points and persist in old patterns of thinking and tired polemics. Some have expressed their frustration with Fuller for his bad judgment. One of these is Michael Lynch, Professor of Science & Technology Studies at Cornell University, who has published several articles condemning Fuller's role as an expert witness in the Dover trial. One of these was in the same journal Spontaneous Generations that carried the essay under consideration here, to which Fuller has recently responded. He pointed out that his "game" is not for short-term gain but for long-term success.

"In that context, I undertake a risky performance in the spirit of a living experiment, the results of which should prove instructive not only to myself but also to others who in the future are similarly well-positioned to bring science studies to bear on public policy. The only mistake would be for others not to repeat the experiment."

Fuller is prepared to criticize Ruse and Pennock for being "traitors to their training" and guilty of "intellectual treason". He is prepared to say that Barbara Forrest's tactic has been to shift the argument from evaluation of ideas to the "intentions of those promoting them", thereby following in the footsteps of John Dewey who used this approach to earn a reputation as "one of the foremost Red-baiters in the US philosophical establishment in the 1940s and '50s". These charges are not ad hominems but are based on analysis of their arguments. The issues are far too important to allow room for complacency - academic freedoms are being eroded, young scientists are fearful of expressing any positive views on design, parental responsibilities for the education of their children are being eroded (with charges of "child abuse" being thrown around), and much more. But Fuller is also prepared to press upon tenured academics the obligation he thinks they have to use their positions of relative security to contribute to public controversies about the nature of science. There is an urgency about the situation. The least that can be said is that Fuller is a trail blazer. No one can criticize him for not acting out what he is encouraging others to do.

Science Studies Goes Public: A Report on an Ongoing Performance
Steve Fuller
Spontaneous Generations, 2(1), (2008), 11-21

First para: I believe that tenured historians, philosophers, and sociologists of science - when presented with the opportunity - have a professional obligation to get involved in public controversies over what should count as science. I stress 'tenured' because the involved academics need to be materially protected from the consequences of their involvement, given the amount of misrepresentation and abuse that is likely to follow, whatever position they take. Indeed, the institution of academic tenure justifies itself most clearly in such heat-seeking situations, where one may appear to offer a reasoned defense for views that many consider indefensible. To be sure, the opportunities for involvement will vary in kind and number, but I believe that we are obliged to embrace them. In the specific case of 'demarcation' questions of what counts as science, the people who possess the sort of general and comparative knowledge most relevant for adducing this matter are historians, philosophers, and sociologists of science - not professional scientists unschooled in these areas.

Response to Lynch
Steve Fuller
Spontaneous Generations, 3(1), (2009), 220-222.

See also:

Lynch, M. Going Public: A Cautionary Tale, Spontaneous Generations, 3(1), (2009), 212-219.

Tyler, D. A "teachable moment" regarding the departure of Michael Reiss, ARN Literature blog (25 September 2008)

Tyler, D. Michael Reiss and the science-religion issue, ARN Literature blog (17 September 2008)

Over the years, there has been much interest in the design of running shoes, with product designers building in protection against impacts and other perceived hazards. However, continuing reports of repetitive strain injuries warrant further research and product re-design. The topic has come to the surface recently with a comparison of the forces experienced by feet of habitually shod versus habitually barefoot runners. It emerges that barefoot runners make contact with the ground in a way that avoids impact-related discomfort and injury.

On the left, a habitually shod Kenyan who is heel-striking; on the right, a Kenyan who has never worn shoes and who is forefoot striking in the way most barefoot runners land. Below are representative force traces (in units of body weight) showing how the two styles of running differ in the force generated when the foot collides with the ground. The barefoot runner lands with no collisional force. (Image: Daniel E. Lieberman, Source here)

As a matter of observation, most habitually shod runners first contact the ground with their heel. This is referred to as heel-striking or rear-foot strike. Modern running shoes have been designed to reduce the impact forces with the help of additional cushioning at the heel. Barefoot runners first contact the ground with the front part of their feet and bend their ankles more as they run. This is referred to as fore-foot or mid-foot strike. This mode of running results in reduced collision forces and enhanced comfort.

"People who don't wear shoes when they run have an astonishingly different strike," says Daniel E. Lieberman, professor of human evolutionary biology at Harvard University and co-author of a paper appearing this week in the journal Nature. "By landing on the middle or front of the foot, barefoot runners have almost no impact collision, much less than most shod runners generate when they heel-strike. Most people today think barefoot running is dangerous and hurts, but actually you can run barefoot on the world's hardest surfaces without the slightest discomfort and pain. All you need is a few calluses to avoid roughing up the skin of the foot. Further, it might be less injurious than the way some people run in shoes."

Since this is a topic where there are numerous agents with commercial interests, the authors of the research paper have felt the need to issue a disclaimer that their reported work is essentially empirical in nature.

"Please note that we present no data on how people should run, whether shoes cause some injuries, or whether barefoot running causes other kinds of injuries. We believe there is a strong need for controlled, prospective studies on these problems." (Source here)

However, the authors go well beyond the empirical data in their analysis when they ground their work in a framework of evolutionary biology. This is also the starting point for Jungers' commentary on the research: "A commitment to walking and running on two legs distinguishes humans from apes, and has long been the defining adaptation of the hominins - the lineages that include both humans and our extinct relatives. This form of locomotion (bipedalism) has been around for millions of years, and we have been unshod for more than 99% of that time." The view, therefore, is that the context for understanding running is that it has evolved as an adaptation under the influence of natural selection.

"Our feet were made in part for running," Lieberman says. But as he and his co-authors write in Nature: "Humans have engaged in endurance running for millions of years, but the modern running shoe was not invented until the 1970s. For most of human evolutionary history, runners were either barefoot or wore minimal footwear such as sandals or moccasins with smaller heels and little cushioning."

There is another perspective on this, which is that of design. Design advocates will affirm: 'Our feet were designed in part for running'. Humans live in many different environments, and the design issues are affected by the need to walk, jump, climb, carry and run in these different environments. A sensitivity to design means that we need to understand how our feet work best in different conditions, so it follows that runners should adopt a biomechanical and physiological approach to developing good running habits. Runners should train to develop the full potential of the design features of their bodies. An evolutionary story of how ape-like animals developed bipedalism is simply a veneer overlying the empirical data.

Foot strike patterns and collision forces in habitually barefoot versus shod runners
Daniel E. Lieberman, Madhusudhan Venkadesan, William A. Werbel, Adam I. Daoud, Susan D'Andrea, Irene S. Davis, Robert Ojiambo Mang'Eni & Yannis Pitsiladis
Nature 463, 531-535 (28 January 2010) | doi:10.1038/nature08723

First para: Humans have engaged in endurance running for millions of years, but the modern running shoe was not invented until the 1970s. For most of human evolutionary history, runners were either barefoot or wore minimal footwear such as sandals or moccasins with smaller heels and little cushioning relative to modern running shoes. We wondered how runners coped with the impact caused by the foot colliding with the ground before the invention of the modern shoe. Here we show that habitually barefoot endurance runners often land on the fore-foot (fore-foot strike) before bringing down the heel, but they sometimes land with a flat foot (mid-foot strike) or, less often, on the heel (rear-foot strike). In contrast, habitually shod runners mostly rear-foot strike, facilitated by the elevated and cushioned heel of the modern running shoe. Kinematic and kinetic analyses show that even on hard surfaces, barefoot runners who fore-foot strike generate smaller collision forces than shod rear-foot strikers. This difference results primarily from a more plantarflexed foot at landing and more ankle compliance during impact, decreasing the effective mass of the body that collides with the ground. Fore-foot- and mid-foot-strike gaits were probably more common when humans ran barefoot or in minimal shoes, and may protect the feet and lower limbs from some of the impact-related injuries now experienced by a high percentage of runners.

See also:

The Barefoot Professor: by Nature Video

Jungers, W.L., Barefoot running strikes back, Nature 463, 433-434 (28 January 2010) | doi:10.1038/463433a

Tyler, D. The human body is built for running, ARN Literature blog (29 October 2009)

Review Of Intelligent Design 101: Leading Experts Explain The Key Issues
ISBN 978-0-8254-2781-7

By Robert Deyes
ARN Correspondent

The debate over whether or not our universe was designed with a purpose is one that centers not around philosophical questions but over "competing scientific explanations of the data". That is the central argument expounded by Phillip Johnson in Intelligent Design 101, a book that aims to bring into sharp focus the central tenets of the intelligent design (ID) movement. Contrary to a popular misconception, the modern day controversy over design in biology is not one that arose from some push to force Judeo-Christian beliefs into the science classroom. It is instead one that extends back thousands of years to the time of Plato and Xenophon in ancient Greece.

Today the educational literature defines all aspects of biology in purely naturalistic terms. What is more, evolution has become the "monolithic fact" that we must all embrace. Even though there is incontrovertible evidence that defies such a factual status, evolutionists have bent over backwards to make naturalism fill in the glaring inconsistencies in the data. As a vociferous opponent of the macro-evolutionary aspects of Darwinism, Johnson has attempted a "divide and conquer" approach to break such a stronghold. By separating philosophical naturalists such as Richard Dawkins from scientists with a sound objective outlook, Johnson's much-publicized Wedge Strategy has sought to prize neo-Darwinism away from its "pedestal of philosophical naturalism". Attacks on Johnson's initiative have focused on the religious backgrounds of its supporters rather than on the sound scientific arguments that they put forward. Still, as Johnson remarks those who today maintain that ID is all about religion ignore the counter claim that the theory of evolution is not exactly all about science.

Addressing this point in a later chapter of the book, philosopher J.P Moreland re-emphasizes a long-standing denial- ID makes no theological commitments to Christianity, Hinduism, Islam or any other religion and does not set us on a "slippery slope" of religious interference of science. Instead ID has scientific legitimacy evidenced by the observation that those who argue against it do so by attempting to falsify its scientific claims.

What are the scientific foundations upon which ID stands? Geologist and lawyer Casey Luskin, biochemist Michael Behe and philosopher Jay Richards remind us of the widely-disseminated ID arguments in their respective chapters of Intelligent Design 101. Complex information-rich objects such as those that lead to the inference of intelligent activity in archaeology and forensic science also exist in the molecular world. Behe builds on Luskin's platform by treating us to an exposition of how irreducible complexity in nano-molecular machines continues to present "a conundrum for Darwinism". Richards then gives us a comprehensive rebuttal of the materialistic interpretation of the Copernican principle challenging science popularizer and television celebrity Carl Sagan's assumption that "the universe is all there is" and listing the features that are necessary for a habitable planet such as our earth to exist. Rather than being winners of a "grand cosmic lottery", our earth's habitability coupled with its prime 'real estate' position for making scientific discoveries argue in favor of design and purpose.

Evolutionary stalwart Julian Huxley famously opened the centennial of the publication of The Origin Of Species with the proclamation that naturalistic evolution explained the totality of life's existence. Nevertheless the more recent struggles between creationists on whether the universe is thousands or billions of years old have done little to quell the rising tide of scientists who feel uncomfortable with the Darwinian endpoint. In Johnson's assessment ID has become the umbrella movement that unites "people of many viewpoints who were once divided on side issues". Today there exists a tremendous dissatisfaction with the Darwinian synthesis amongst reputable scientists who are unconvinced by the supposedly unarguable evidence that Darwinists hold on to. Within such a setting, Johnson equates his volume Darwin On Trial to "a match that lit the tinder beneath a stockpile of logs".

In his chapter entitled Philosophical Implications Of Neo-Darwinism and Intelligent Design, philosopher Eddie Colanter brings to the reader's attention the religious undertones of the so-called strong form of Neo-Darwinism which holds that (i) all of life is the product of purely materialistic forces, (ii) any reference to God is superfluous and (iii) any moral values that humans place on their comportment are purely arbitrary and subjective (this latter point has important ramifications for how we view contemporary social issues such as abortion, euthanasia and the definition of personhood).

Intelligent Design 101 then concludes with a broad overview of the historical landscape upon which ID has made its impact. What is made explicit is that ID is not simply a modern extension of the Christian creationism that featured in prominent legal cases such as those surrounding the Tennessee anti-evolution laws of the 1970s. In the words of distinguished theologian H Wayne House, it is a movement that carries with it an "empirical method of argument [and a] lack of allusion to the fundamentalist wing of Christianity and Christian theology".

As we approach Darwin day with its accompanying festivities and plans to parade his namesake through museum halls across the nation, we cannot ignore the vast body of evidence that today is feeding the ID counter-attack. Intelligent Design 101 is an invaluable resource for those seeking to understand the twisted fables of the anti-ID lobby. If those who oppose ID have nothing to fear, they should be prepared to entertain competing points of view and to let truth and reason become "the final arbiters".

2010 sees the beginning of a new series in Spanish exploring key findings from contemporary science that support the intelligent design inference. The series Passeos Por La Naturaleza (A Walk Through Nature) aims to further strengthen the global influence that the Intelligent Design movement already enjoys and raise awareness of important academic resources that are today challenging orthodox Darwinism and revitalizing the call for a fresh perspective on scientific discourse.

First installment can be found at:

Paseos Por La Naturaleza

Evolucion de la comunicacion en las ballenas? Los darwinistas deberian estar preocupados, by Robert Deyes and Carolina Deyes (transl: Whale Evolution? Darwinist 'Trawlers' Have Every Reason To Be Concerned)

by Denyse O'Leary
ARN correspondent

Here is my post at Examiner on why. I thought it would never happen, actually. But I should have remembered - all psychology fads are inherently ridiculous because they are attempts to evade the depth of the human condition with some silly new idea.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

The first species to have its genome decoded by 'next-generation-sequencing' (NGS) machines is the giant panda (Ailuropoda melanoleuca). The individual animal was known previously to the world as the mascot of the 2008 Beijing Olympic Games. Scientists have been excited by the report because the NGS approach is significantly cheaper and faster than other methods. It is not the purpose of this blog to assess the robustness of the method, but it is important to be aware that the reported sequence utilizes previously determined genomes as a reference platform: dog and human genomes in this case.

"Using evidence-based gene prediction, the human and dog genes [. . .] were projected onto the panda genome, and the gene loci were defined by using both sequence similarity and whole-genome synteny information."

The iconic giant panda's genetic makeup reveals degradation (Source here)

The estimated size of the giant panda genome is said to be 2.40 Gb (compared with 2.45 Gb for the dog genome and 3.0 Gb for humans) making up about 21,000 genes (similar to humans). "Overall, we found that the quality of the predicted panda genes was comparable to that of other well-annotated mammalian genes." Although the panda eats only bamboo leaves, genes associated with carnivory are present in the panda:

"Of interest, our analysis of genes potentially involved in the evolution of the panda's reliance on bamboo in its diet showed that the panda seems to have maintained the genetic requirements for being purely carnivorous even though its diet is primarily herbivorous."

There was no trace of genes that encode enzymes for digesting cellulose, raising questions about how the panda can possibly survive on bamboo. The hypothesis proposed is that the bamboo diet "may instead be more dependent on its gut microbiome". Confirmation of this will require further work. A related dietary factor concerns the sense of taste. The authors refer to the five components of taste: sweetness, saltiness, sourness, bitterness and umami. The giant panda has lost the capability of sensing umami, which means that meat has become unappetizing.

"Umami is sensed through the T1R family. In the panda genome, T1R2 and T1R3 are in an intact form, but T1R1 has become a pseudogene - we found that [. . .] two panda T1R1 exons contain transcript errors."
"Two frameshift mutations occurred in the third and sixth exons of the panda T1R1 gene. The third exon contained a 2-bp ('GG') insertion; the sixth exon contained a 4-bp ('GTGT') deletion."

A possible genetic factor affecting the giant panda's low fecundity rate was identified. Nearly all of the mammalian reproduction genes were mapped, and "a putative pseudo follicle-stimulating hormone (FSH) [beta]-subunit gene (giant panda-FSHB2)" was noted. The authors comment:

"At this stage, whether the pseudo FSHB2 gene contributes to the reproduction features of the giant panda remains to be determined."

Some have considered whether the panda genome helps resolve the animal's taxonomic status. Although most place the panda in the bear family (Ursidae), a case has been made that it belongs elsewhere - in the raccoon family (Ailuridae). Since we do not have the genomes for any of these possible relatives, there is little more that can be said on the matter. However, even if other genomes were sequenced, does the "genome" tell us much about what makes a bear differ from a raccoon or a dog or a human? The genome can be described as the repository of housekeeping genes; it provides the materials needed for the organism to function - but something much more than this is needed to inform taxonomy. The ENCODE project (along with many others) has revealed rich functionality in the non-coding DNA (alias 'junk DNA'). Consequently, it is probable that the gene sequencers are just scratching at the surface of genetic information.

If the giant panda is correctly assigned to the Ursidae, the new research contributes significantly to the way we understand the speciation of this animal. Before genome sequencing, we could say that it has diversified significantly from ancestral Ursidae stock. It has a reduced number of chromosomes, 42, whereas most bears have 74. It has a wholly vegetarian diet and it has a modified sesamoid bone which it uses to strip bamboo leaves from stems. The panda genome findings provide the background for understanding herbivory: the panda still retains the genes for carnivory but mutations have destroyed the taste trigger for it to eat meat. Although the panda cannot make enzymes for digesting plant food, communities of gut microbes are the most likely explanation of its continuing survival. The reproduction problems experienced by giant pandas may also be linked to a mutation affecting follicle stimulation.

The overall picture is one of speciation/diversification linked to genetic degradation. Natural selection, which has often been portrayed as all-powerful and capable of building exquisitely complex structures, has failed to provide the giant panda with any enzymes for digesting plant food. We do not know whether the modified sesamoid bone is an evolutionary innovation, a part of the degradation story or information neutral. The News & Views essay that accompanies the research paper calls the panda China's "national treasure" - and so it is. However, from the perspective of genetics, the giant panda is not in a healthy state. Whatever else may be relevant, this case has strong affinities with speciation by gene pool reduction. From the perspective of Darwinism, the giant panda genome testifies to the failure of Darwinian mechanisms to overcome problems caused by mutations. From the perspective of design, we have a story of how a superbly designed carnivore has managed to survive the effects of genetic degradation. From a conservation perspective, without human intervention, the chances of long-term survival are slender.

There is also the finding that Jingjing's genome has a high degree of genetic diversity, but she is unlikely to be representative of the panda population taken as a whole. It is more prudent to assume that the relatively isolated panda enclaves harbour problems of inbreeding and that Jingjing is an example of the benefits of breeding across enclaves - further supporting the case for human intervention.

The sequence and de novo assembly of the giant panda genome
Li, R. et al.
Nature 463, 311-317 (21 January 2010) | doi:10.1038/nature08696

Abstract: Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

See also:

Worley, K.C. and Gibbs, R.A. Decoding a national treasure, Nature 463, 303-304 (21 January 2010) | doi:10.1038/463303a

Qiu, J., Genome reveals panda's carnivorous side, 13 December 2009, Nature News | doi:10.1038/news.2009.1141

The debate between Darwin and design is coming to Tampa, Florida with a major one-night event featuring some of the leading voices challenging Darwinian evolution...Michael Medved, Stephen C. Meyer, David Berlinski. The event will occur Thursday evening, January 28th.

Info HERE...

by Denyse O'Leary
ARN correspondent

David Warren is a Canadian journalist who writes for the Ottawa Citizen. He often expresses skepticism about Darwinism. Here he reflects on the "just-so" story usually used to explain Darwinian evolution:

The account of the Beginning of the Armadilloes, in the High and Far-Off Times -- and on the banks of the turbid Amazon -- is especially instructive. It supplies a theory of the convergent evolution of the clever armadillo, from the Stickly-Prickly Hedgehog and/or his friend the Slow-Solid Tortoise, under the ministrations of the Painted Jaguar.

Consulting it today, I realize that my skepticism toward the dogmas of neo-Darwinism might well originate from that story. It is not that I prefer Kipling's account of the origin of species, which was a quite intentional (and very amusing) farce. Rather, that it spared me from developing a taste for quite unintentional farces.

In logic, a "just-so story" is known as the "ad hoc fallacy." The Latin means "for this," and it applies to any "pourquoi" explanation of things, given for the express purpose of supporting an otherwise unprovable hypothesis.

The perfect example would be the whole pseudo-science of "evolutionary psychology," which seeks to explain why man is the way he is, by means of evolutionary plausibilities. We start from the hypothesis that everything in nature, as Darwin says, adapts exclusively to the end of survival. And then we return to the same place, by a logical circle.

Here are more of Warren's columns on this subject. (The first one begins with a reader's letter on one of his columns.)

Here are more stories on evolutionary psychology.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

In ENV...Discovery Institute is gearing up for the celebration by supporting what Darwin supported: academic freedom.

Academic Freedom Day couldn't come at a better time, as academic freedom is threatened around the country. We have seen Darwinists launch cyber attacks on a pro-ID conference website in Colorado and engage in an illegal coverup in the censorship of a pro-ID film in California.

It's time like these when Darwin's own words should instruct everyone on how to have an open and honest debate over evolution and intelligent design.
In On the Origin of Species, Darwin wrote, "A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question." This quote is the cornerstone of the Institute's Academic Freedom Day efforts.

More...

Academic Freedom Update: California Science Center Engaged in Illegal Cover-Up

This episode of ID the Future features an academic freedom update on the California Science Center's cancellation last October of a screening of a pro-ID film, Darwin's Dilemma, by a private group. How does a government agency try to evade its obligations to the First Amendment? By suppressing information. Listen in to learn about the evidence that the Discovery Institute has uncovered in its lawsuit against the Science Center.

Go here to listen.

Well, of course they cancelled it. I cannot imagine why anyone would doubt that outcome.

Look, when I first started blogging - the only real news media today - I had to deal with the controversy over the Smithsonian withdrawing support for the screening of Privileged Planet. Go here for more.

But the Smithsonian was the famed institution where Walcott basically did nothing for decades about the critical evidence from the Cambrian evolution that showed that Darwinism is wrong.

If that's the science we want, fine. Our taxes pay for it.

Another podcast:

Rodney LeVake: Expelled Science Teacher, Part 1

On this episode of ID The Future, CSC's Casey Luskin interviews Rodney LeVake, the plaintiff in the Academic Freedom court case LeVake vs. Independent School District #656. LeVake, a former high school biology teacher, informally expressed doubts about evolution to a colleague who then reported him to the principal. LeVake ended up losing his biology position, not because he taught creationism or intelligent design, but merely because he expressed reservations about evolution to a colleague. Listen as he tells his story of clear academic persecution.

Go here to listen.

But what else is new? If LeVake had expressed doubts about the decline of bears* in Canada, he would have run into the same problem. Once a supposed "science" theory has become a big time theory-a-rama, you don't need evidence. You just need to keep inciting the base of people who are either paid or pay to support you. And administration is easily cowed.

So why don't they all seek work in the dairy industry?

The claim that Rubisco is poorly designed or unintelligently designed was appearing in textbooks in the 1990s. The idea has been picked up recently in a News & Views piece by John Ellis. He writes that Rubisco "is a relic of a bygone age" and his essay has the title: "Tackling unintelligent design".

"Rubisco is the most important enyzme on the planet - virtually all the organic carbon in the biosphere derives ultimately from the carbon dioxide that this enzyme fixes from the atmosphere. But Rubisco is also one of the most inefficient enzymes on the planet. It evolved when the atmospheric composition was different from that of today, and its failure to adapt significantly to the modern atmosphere limits agricultural productivity."

RuBisCO has an active site (binding pocket) that binds ribulose-1,5-bisphosphate (RuBP) and catalyzes the reaction between RuBP and CO2 or O2. In the figure, the two large RuBisCO subunits (blue and cyan) sandwich an RuBP molecule (orange) in the active site. The site is gated by the C-terminus (yellow), lysine 128 (purple), and loop 6 (green), which undergo periodic conformational changes that open or close the site. Reactants enter and products escape while it is in an open state, and carbon-fixation reactions occur during the closed state. (Image credit: Paul Crozier, Sandia National Labs. Source here)

Over the past decade, the pendulum has swung away from the idea that Rubisco is unintelligent design. Its achievements are remarkable, as Griffiths (2006) explains:

"It is curious that Rubisco should fix CO2 at all, as there is 25 times more O2 than CO2 in solution at 25 degC, and a 500-fold difference between them in gaseous form. Yet only 25% of reactions are oxygenase events at this temperature, and carbon intermediates 'lost' to the carbon fixation reactions by oxygenase action are metabolized and partly recovered by the so-called photorespiratory pathway. Catalysis begins with activation of Rubisco by the enzyme Rubisco activase, when first CO2 and then a magnesium ion bind to the active site. The substrate, ribulose bisphosphate, then reacts with these to form an enediol intermediate, which engages with either another CO2 or an O2 molecule, either of which must diffuse down a solvent channel to reach the active site."

The analysis of Tcherkez et al. (2006) was significant for showing that Rubisco does not bear the marks of Darwinian tinkering and that research to genetic modify the enzyme to gain agricultural benefits can be expected to deliver only "modest improvements" in its efficiency of operation.

"Further, [our hypothesis] raises the possibility that, despite appearing sluggish and confused, most Rubiscos may be near-optimally adapted to their different gaseous and thermal environments. If so, genetic manipulation can be expected to achieve only modest improvements in the efficiency of Rubisco and plant growth. Such improvement would be limited to the magnitude of the scatter apparent in the correlations (Fig. 3), if the scatter represents incomplete optimization (see above). [. . .] Such adaptation in response to the changing atmosphere and temperature appears to have been instrumental in enabling the expansion of the biosphere to its current size."

Design theorists have drawn attention to three additional considerations:
1. A single-factor analysis of Rubisco is inadequate. The parameters considered to conclude the enzyme is poorly designed and inefficient are very limited. We should note that our perceptions of intelligent design are typically subjective, and most claims for poor design do not stand up to the test of time - further research leads to a greater appreciation of design (a good example being mammalian eye design). Furthermore, unintelligent design of architectures we deem sub-optimal should not be regarded as the only possible hypothesis. Multiple factors are likely to be relevant as chemosynthetic carbon fixation also makes use of Rubisco. It is employed by organisms living at hydrothermal vents and cold hydrocarbon seeps.
2. Photorespiration, the consumption of oxygen to produce a sugar that ultimately forms carbon dioxide during a series of reactions, may not be a mark of inefficiency, but the process may be useful to the plant. The null hypothesis for Design theorists is that processes have functionality. This hypothesis is not without some support: the process of photosynthesis is not just to capture CO2 and release oxygen because nitrate assimilation in plant shoots depends on photorespiration, as Rachmilevitch et al (2004) have shown.
3. Ecological considerations should be included in the analysis. If design is relevant to understanding the way plants work, we should consider not only the benefits to the organism (which limits the horizon for those with a Darwinian perspective) but also the biosphere as a whole. Rubisco's ability to capture CO2 increases with increasing CO2 content in the atmosphere, so its efficiency rises in a CO2-rich atmosphere. However, increasing oxygen levels in the atmosphere will reduce Rubisco's ability to capture carbon. So a negative feedback mechanism exists to regulate the relative concentrations of oxygen and carbon dioxide in the atmosphere. This is another example of design affecting the Earth's ecology - for more on this, go here.

Ellis was commenting on a paper by Liu et al. that reports on work to produce a Rubisco in vitro. In order to do this, the authors required two chaperone proteins, ATP and addition of 18 protein subunits (taken from a cyanobacterial Rubisco) to be introduced in the correct sequence to get yields of the enzyme. It is hoped that this procedure can be used to produce mutated versions that can be screened for improved effectiveness. It's all very interesting, but the biggest mystery is why people who expend so much intellectual energy on improving this remarkable molecule can live with the thought that "Rubisco is a superb example of unintelligent design for the modern world". Maybe research funds would be better spent exploring avenues identified using the presumption that this enzyme is optimally designed.

Tackling unintelligent design
R. John Ellis
Nature 463, 164-165 (14 January 2010) | doi:10.1038/463164a [restricted link]

Abstract: The key enzyme in photosynthesis, Rubisco, is a relic of a bygone age. The ability to assemble Rubisco in the test tube offers the prospect of genetically manipulating the enzyme to make it fit for the modern world.

Coupled chaperone action in folding and assembly of hexadecameric Rubisco
Cuimin Liu, Anna L. Young, Amanda Starling-Windhof, Andreas Bracher, Sandra Saschenbrecker, Bharathi Vasudeva Rao, Karnam Vasudeva Rao, Otto Berninghausen, Thorsten Mielke, F. Ulrich Hartl, Roland Beckmann & Manajit Hayer-Hartl.
Nature 463, 197-202 (14 January 2010) | doi:10.1038/nature08651 [restricted link]

Abstract: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO2 in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX2. RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX2. As revealed by the structure of a RbcL8-(RbcX2)8 assembly intermediate, RbcX2 acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL8 core assembly. Finally, addition of RbcS results in RbcX2 release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.

See also:

Griffiths, H., Designs on Rubisco, Nature 441, 940-941 (22 June 2006) | doi:10.1038/441940a [restricted link]

Rachmilevitch, S., Cousins, A.B., Bloom, A.J., 2004. Nitrate Assimilation in plant shoots depends on photorespiration. Proceedings of the National Academy of Sciences USA, 101(31), 11506-11510 | doi: 10.1073/pnas.0404388101 [abstract]

Tcherkez, G.G.B., Farquhar, G.D. and Andrews, T.J., Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized, Proceedings of the National Academy of Sciences USA, May 9, 2006, 103(19), 7246-7251 | doi: 10.1073/pnas.0600605103 [abstract]

by Denyse O'Leary
ARN correspondent

This contest seemed to have attracted a lot of discussion, with 148 entries, so I spent all yesterday getting through the entries. Its basis was a fawning review by David B. Hart, of Richard Dawkins's The Greatest Show on Earth. We are informed - on the mag’s cover - that Dawkins "gets a gold star" for his book of that name (January 2010 Number 199).

Well, Darwinism is certainly one of the greater shows on Earth, and Dawkins is worthy a life membership in an illusionists' association.

The winner this time is Paul Giem at 111 (minor correction offered at 112), for

To come back to the point of this post, we were asked to critique the comment,

The best argument against ID theory, when all is said and done, is that it rests on a premise - irreducible complexity" - that may seem compelling at the purely intuitive level but that can never logically be demonstrated. At the end of the day, it is – as Francis Collins rightly remarks – an argument from personal incredulity. While it is true that very suggestive metaphysical arguments can be drawn from the reality of form, the intelligibility of the universe, consciousness, the laws of physics, or (most importantly) ontological contingency, the mere biological complexity of this or that organism can never amount to an irrefutable proof of anything other than the incalculable complexity of that organism's phylogenic antecedents.

My reply:

There are several problems with this paragraph. For example, there is the idea that ID rests on the premise of irreducible complexity. In fact, the origin of life is a far stronger foundation for ID (see Signature in the Cell), and the Privileged Planet hypothesis does not need irreducible complexity.

Another problem is the difficulty with the last sentence. If the "biological complexity" of an organism is "an irrefutable proof" of the "incalculable complexity" of its progeniters, and their progenitors had it, and so forth, did the incalculable complexity come from an originally "Incalculably complex" organism which arose spontaneously, or was the "irrefutable proof" somehow violated somewhere, or multiple times? Or does the concession constitute a proof of ID, in spite of the author's protestations?

But the part of the argument that stands out as the worst is the assertion that irreducible complexity "may seem compelling at the purely intuitive level but that can never logically be demonstrated." At this point I feel like I'm watching a movie, where the villain has been tracked down by the detectives who have put the clues together, and suddenly switches from pretending innocence to saying, "You can’t prove a thing!" He has now lost the audience (including any remaining doubt in the detectives). All that remains is the power play and the legal maneuvering. We now know the truth of his villainy to a moral certainty.

Science has never been about proof, and those who expect to attack ID because it can't be proved have committed a category error. The fact that they have to resort to this kind of argument suggests a fundamental weakness in their position.

Nor is the appeal to the supposed fallacy of "personal incredulity" helpful. What is the opposite? "Personal credulity?" If the contest is between faith and skepticism, it would seem that the proper scientific attitude would be skepticism.

There are other mistakes, but this belief that ID must be wrong until it can "logically be demonstrated" is obtained is the worst. If that's the "best argument against ID theory", then ID has it made.

I appreciated his point that science is about evidence, not "irrefutable proof". The latter is the domain of pure mathematics. (Why we cannot square a circle or meaningfully divide by zero.) But statistics and information theory are about the balance of evidence, and if the evidence does not support the idea that Darwinism creates much information, then it is not a good theory.

A free copy of Expelled goes to him, on condition of providing me with a working postal address, at oleary@sympatico.ca ]

I also appreciated Jerry's thoughtfulness in 137 through 139.

Further comments:

Just about everything Hart said about intelligent design theory, as quoted by Giem above, is wrong, and that is not an easy feat. It is hard to know where to begin, with stuff like this. For one thing, what is wrong with "purely intuitive level" and "personal incredulity"? If a landlady thinks that her drunken boarder will not pay his rent come Friday, though he swears up and down he will, that is a purely intuitive level of personal incredulity. She cannot predict the future because she is not God Almighty. But she is probably right anyway in her assessment, and should act on it.

And the rest is just bafflegab. For more on "bafflegab" (a term I did NOT invent), see below.

Go here for more.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

Dr. William Dembski, internationally known as a paradigmatic figure in the world of science - particularly as he has advanced the theory of intelligent design regarding the creation of the world in contrast to Darwinian evolution is featured on a recent PODCAST. The subject is his recent book - The End of Christianity: Finding a Good God in an Evil World.

More...

Frank Turek, of (http://www.CrossExamined.org) and much more, will have an internet radio talk show on Tuesday, January 19th, beginning at 7 p.m. CENTRAL time. His guests will be some of the top apologists in the world.

The evening will start with the man who is one of the best debaters in the world, Dr. William Lane Craig www.ReasonableFaith.org.

Next will be one of the founding fathers of the Intelligent Design movement-- Dr. Bill Dembski www.designinference.com. He'll show us very simply how life points to an intelligent designer, and how most of the so-called "evidence" for macroevolution is based on materialistic and counter-factual philosophical assumptions.

Next will be Dr. Mike Adams, a Christian professor on a secular campus and one of the most popular conservative columnists on www.Townhall.com.

The show will be capped off with Josh McDowell www.Josh.org. Josh will give us very helpful insights on the importance of relationships to a young person's faith.

A listing of the 200 stations carrying the program can be found here (http://action.afa.net/Radio/). For the live web simulcast, go here: http://action.afa.net/Webcast/WebcastPlayer.aspx?id=2147491014
The American Family Association, who are producing this event, will create a DVD of the program that will be available afterwards. Check www.CrossExamined.org later for details.

ENV reports that Senate Minority Leader Dennis Hollingsworth has sent a letter to the California Science Center (CSC) requesting documents related to the Center's cancellation of a screening last October of the pro-intelligent design documentary "Darwin’s Dilemma." The screening was sponsored by the American Freedom Alliance (AFA), a private group that had rented the Center's IMAX theater.

Senator Hollingsworth's letter follows two lawsuits filed against the state government-operated Science Center charging that it violated both the First Amendment and California's open records law in its effort to stop the screening and then cover up the real story behind the cancellation.

More...

As reported in ENV, Dr. Atkins, is a noted critic of intelligent design and author who appeared in Expelled, stating: "Religion, it's just fantasy...and is evil as well." According to a 1992 article by Atkins in New Scientist, "Darwin effectively swept purpose aside in the living world," and "[a]ll reimpositions of purpose are artifices of the religious to feed their faith." He holds little back on religion, claiming that it only offers only "empty gulping and the verbal flatulence that passes for theistic exposition."

More...

by Denyse O'Leary
ARN correspondent

I just came across this fact in the journal Nature: Little is known about human evolution other than basic outline.

So, contrary to widely heard huffing, there are huge gaps in our understanding of early humans. In Nature's 2020 Visions (7 January 2010) Scroll down to Leslie C. Aiello, and we learn

Most of the recent effort in hominin palaeontology has been focused on Africa and Europe. But the announcement in 2004 of the small hominin Homo floresiensis in Indonesia was a warning that we are naive to assume we know more than the basic outline of human evolutionary history. If H. floresiensis is indeed a surviving remnant of early Homo that left Africa around 2 million years ago, we have to reject the long-standing idea that Homo erectus was the first African emigrant. We also must reject many hypotheses concerning the prerequisites for this emigration, such as a relatively large brain size, large body size and human-like limb proportions. Importantly, we must confront our relative ignorance about human evolution outside Europe and Africa.- "Hominin paleontology"

Now, I don't believe for a moment that 2020 is going to yield a whole lot more information, as Mr. Aiello* hopes - more likely a whole lot more grant applications, as more people graduate and need a focus for their work.

That doesn't mean the work isn't worth doing. It does, however, raise a key question: Why are people expected to learn in school whatever evolution story is currently taken seriously - by whomever and for whatever reason?

When I was in school fifty years ago, we struggled through polynomials, the life cycle of the common toad, and how to behave on stage when putting on a fragment of Shakespeare's Julius Caesar - facts that were not under dispute and unlikely to change in the lifetime of anyone present.

Anyway, courtesy of the Discovery Institute, I have a copy of David Berlinski's The Deniable Darwin, for the best answer to the question: Why is human evolution, in its actual present state, compulsorily taught in schools? Why are people going to court in order to force the teaching?

Here are the contest rules. Winners get a certificate as well as the prize. You do not need to give me your actual address, just an address I can send the prize to, and we never save addresses for a mailing list.

*Aiello is President, Wenner-Gren Foundation for Anthropological Research

Go here to enter.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

"It seems we have all been guilty of defaming Neanderthal man" declared a recent Editorial in The Guardian. This comment was triggered by a report documenting evidence for the use of pigments and decorative shells by Neanderthals. This is claimed to have occurred many years before any direct contact with modern humans, thereby undermining any thought that the artefacts did not really represent Neanderthal culture. Personal adornment, using a variety of colours, implies an aesthetic sense and an appreciation of symbolism. Since Neanderthals have often been presented as lacking these "modern" traits, the new research demands a reappraisal.

This decorative shell likely adorned the neck of a Neanderthal (Image credit Joao Zilhao, Source here)

It may be helpful to describe the findings by reference to a design methodology. Two archaeological sites from the Murcia province of southern Spain have yielded artefacts. Apart from the usual stone tools and hearth features, there are a variety of perforated shells and a striking range of coloured pigments. Elsewhere in the world, such finds are associated with personal ornamentation.

Red coloured pigments are made from mixtures of siderite, goethite, hematite and nontronite. Yellow coloured colorants were of siderite and natrojarosite. These minerals are not found at levels where they could be collected by Neanderthals in the immediate environment, although the authors report sources for the red materials 3-5 km to the northwest, and the closest source for the yellow materials is 7 km to the east. The options are: Law (the minerals were deposited by hydrothermal processes locally); Chance (the materials have been carried to the area by water flow or some other mechanism) and Design (Neanderthals sourced the pigments and brought them to the site). However, after considering pros and cons of these options, the authors are in no doubt about the implications. They conclude: "These pigments can only be manuports". The Design inference is the most parsimonious.

A similar, but more complex, analysis of the perforated shells was made. The authors find no essential difference between their Spanish material and other finds from Africa and the Near East where the "symbolic implications of body painting and of the ornamental use of pigment-stained and perforated marine shells are uncontroversial". This has led to the authors claiming a high degree of confidence in their conclusions about the "modern" behaviour of Neanderthals. According to BBC News:

"Professor Zilhao explained that the findings were dated at 10,000 years before any contact between Neanderthals and modern humans. "To me, it's the smoking gun that kills the argument once and for all," he told BBC News. "The association of these findings with Neanderthals is rock-solid and people have to draw the associations and bury this view of Neanderthals as half-wits.""

Once the implications of the new research sinks home, a different light is shed on previously reported cultural artefacts. Take, for example, the occurrence of "pierced and grooved animal teeth in Neandertal-associated archeological cultures (such as the Chatelperronian of France)". Because of contemporaneous modern humans, this has been explained by "stratigraphic mixing" or "imitation without understanding". However, it could equally well be explained as "independent Neandertal innovation". This is the conclusion reached by the lead author and his team:

"When considering the nature of the cultural and genetic exchanges that occurred between Neanderthals and modern humans at the time of contact in Europe, we should recognise that identical levels of cultural achievement had been reached by both sides." (source here)

We have had a long-sustained exposure to the idea that Neanderthals were sub-human. They have been presented as slow, lumbering, dim-witted and brutish! Most people are likely to think that Neanderthals could not use words to speak. Will the new research change perceptions?

"It's very difficult to dislodge the brutish image from popular thinking," Professor Stringer told BBC News. "When football fans behave badly, or politicians advocate reactionary views, they are invariably called 'Neanderthal', and I can't see the tabloids changing their headlines any time soon."

The situation we find ourselves in has come about because the Darwinist explanation of human origins has been adopted by our culture. The Darwin origins myth requires a gradual evolution of both anatomy and culture - from ape to man. Neanderthal Man has been part of this story - he is the archetypal intermediary. Despite many evidences to the contrary, little has been done to remove the myth. Indications of cultural sophistication were interpreted as Neanderthals trading artefacts with modern humans, or imitating without understanding. This is a good example of 'saving the paradigm' in a Kuhnian sense, whereby the old paradigm clings on by force-fitting contrary evidences into the accepted theoretical model. It is time to discard the Darwinian mindset that presupposes gradual evolution. Let researchers be free to approach the evidence with multiple working hypotheses and engage in a more rigorous programme of hypothesis testing and analysis.

Symbolic use of marine shells and mineral pigments by Iberian Neandertals
Joao Zilhao, Diego E. Angelucci, Ernestina Badal-Garcia, Francesco d'Errico, Floreal Daniel, Laure Dayet, Katerina Douka, Thomas F. G. Higham, Maria Jose Martinez-Sanchez, Ricardo Montes-Bernardez, Sonia Murcia-Mascaros, Carmen Perez-Sirvent, Clodoaldo Roldan-Garcia, Marian Vanhaeren, Valentin Villaverde, Rachel Wood and Josefina Zapata
Proceedings of the National Academy of Sciences, published online before print January 11, 2010 | doi:10.1073/pnas.0914088107

Abstract: Two sites of the Neandertal-associated Middle Paleolithic of Iberia, dated to as early as approximately 50,000 years ago, yielded perforated and pigment-stained marine shells. At Cueva de los Aviones, three umbo-perforated valves of Acanthocardia and Glycymeris were found alongside lumps of yellow and red colorants, and residues preserved inside a Spondylus shell consist of a red lepidocrocite base mixed with ground, dark red-to-black fragments of hematite and pyrite. A perforated Pecten shell, painted on its external, white side with an orange mix of goethite and hematite, was abandoned after breakage at Cueva Anton, 60 km inland. Comparable early modern human-associated material from Africa and the Near East is widely accepted as evidence for body ornamentation, implying behavioral modernity. The Iberian finds show that European Neandertals were no different from coeval Africans in this regard, countering genetic/cognitive explanations for the emergence of symbolism and strengthening demographic/social ones.

See also:

Tyler, D. Images of evolution as secular icons, ARN Literature Blog (10 April 2009)

Tyler, D. The cognitive skills of Stone Age Man, ARN Literature Blog (29 June 2009)

Tyler, D. Darwinist thinking on the origin of religion, ARN Literature Blog (9 November 2009)

By Robert Deyes
ARN Correspondent

In their book The Privileged Planet, astronomer Guillermo Gonzalez and philosopher of science Jay Richards point out that rather than adopting the original definition of 'science' as a search for knowledge (literal translation from Latin), some opinion makers in science have taken it to mean "applied naturalism" defined as, "the conviction that the material world is all there is, and that chance and impersonal natural law alone explain, indeed must explain, its existence" (1).

Outspoken neo-atheists such as chemist Peter Atkins actively push their materialistic views via the 'scientism' movement, unwaveringly maintaining that science is "the only reliable way we have of discovering anything about the workings of nature and fabric of the world" (2). Philosopher Eddie Colanter described scientism as "the worldview [that] asserts that the only type of truth or knowledge that exists or that is important is that which can be known or verified through the scientific method" (3). Theologian J.P Moreland likewise defined scientism as "the view that science is the very paradigm of truth and rationality" (4).

Notable in Atkins's collective 'house of horrors' is the ontological reductionist notion that metabolic processes alone organize the "random electrical and chemical currents in our brains" that then shape our personalities and creative drive (2). Brain biologist John Eccles revolted against the demeaning undercurrent of such reductionism "with its claim [that] promissory materialism accounts for all the spiritual world in terms of patterns of neuronal activity" (5). In his Challenges From Science theologian John Lennox maintains that if Atkins's assertion were true, it would at once render philosophy, ethics, literature, poetry, art, and music irrelevant for our understanding of reality (6).

Besides throwing these and other disciplines into the intellectual trash heap, Atkins's position better reflects his atheist tendencies than any truly unbiased approach to discussion. His own 'cosmic bootstrap', the idea that cosmic spacetime brought about its own existence and today "generates its own dust in the process of its own self assembly" (6), is laughable precisely because, as theologian Keith Ward notes , "it is logically impossible for a cause to bring about some effect without already being in existence" (6).

Moreland brilliantly counters the axioms that Atkins holds dear by demonstrating their self-refuting nature. "A proposition", writes Moreland "is self-refuting if it refers to and falsifies itself. For example, "There are no English sentences" and "There are no truths" are self-refuting" (4). He later adds that "scientism is not itself a proposition of science, but a second-order proposition about science to the effect that only scientific propositions are true or rational to believe" (4).

Atkins's condemnation of cosmic purpose and design is all too evident in his own rhetoric. "Our universe" he assures us, "hangs there in all its glory, wholly and completely useless. To project onto it our human-inspired notion of purpose would, to my mind, sully and diminish it" (2). Side-stepping the extraordinary nature of the cosmic Big Bang (6), Atkins then contents himself with speculation over the existence of infinite universes (2), and clearly unveils to his audience that his acceptance of the facts is dependent on his own pet peeves and preferences. In short his conclusions are not those of an unsullied objectivist.

Years ago astrophysicist Kenell Touryan warned us of the 'trap of scientism' that, in the realm of biology at least, has become the philosophical foundation of many an evolutionist. "No reputable physicist or chemist" Touryan noted "would be presumptuous enough to characterize scientific discoveries, at least in the hard sciences, as "truth that will make us free"" (7). Laying out the reality of his own experiences he wrote:

"I and many of my physicist colleagues see intelligent design everywhere in nature and, compelled by the weight of such evidence, choose to believe that we are made "a little lower than the angels"... We should all take seriously the principle that "the confidence expressed in any scientific conclusion should be directly proportional to the quantity and quality of evidence for the conclusion"" (7).

Last year's scathing allegation from Atkins and his ilk- that you cannot be a true scientist in the 'deepest sense of the word' and still have religious beliefs (8) - was not one grounded upon scientific insights but on a pervasive atheistic brand of religion. It is high time that we recognized this and tossed the 'addled eggs' of scientism out of the frying pan.

Literature Cited
1. Guillermo Gonzalez and Jay Richards (2004) The Privileged Planet, How Our Place In The Cosmos Is Designed For Discovery, Regnery Publishing Inc, Washington D.C, New York, p.224

2. The Joy Of Science, The Existence Of God And Galileo's Finger, Roger Bingham Interviews Chemist Peter Atkins, 2007, See http://thesciencenetwork.org/media/videos/3/Transcript.pdf

3. Michael Behe, Eddie N. Colanter, Logan Gage, and Phillip Johnson (2008) Intelligent Design 101: Leading Experts Explain The Key Issues, Kregel Publications, Grand Rapids, Michigan, p.161

4. Ibid, p. 204

5. John C. Eccles (1991) Evolution of the Brain, Creation of Self, Published by Routledge, New York, p.241

6. John Lennox (2007) Challenges From Science, Beyond Opinion, Living The Faith We Defend (Ed. Ravi Zacharias), pp. 112-118

7. Kenell J. Touryan (1999) Science and "Truth", Science, 30 July 1999, Volume 285. p. 663

8. Gene Russo (2009) Balancing Belief And Bioscience, Nature Volume 460, p. 654

Access Research Network has just released its annual "Top 10 Darwin and Design Science Stories" for 2009.

Gaining top honors on the list was a peer-reviewed article by intelligent design theorists William Dembski and Robert Marks II in the September 2009 journal IEEE Transactions on Systems, Man and Cybernetics. The authors used computer simulations and information theory to challenge the ability of neo-Darwinian processes to create new functional genetic information. This research provides validation for the core ideas in Dembski's 2001 book No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence. "For years the scientific establishment has tried to brush off intelligent design claiming that there are no peer-reviewed scientific articles supporting the theory and no research being done from the intelligent design paradigm," stated ARN Executive Director, Dennis Wagner. "This article is yet another rebuttal to both charges, and the research results put the monkey squarely on the back of the scientific materialists' to prove Darwinian processes can actually create new functional genetic information" Wagner concluded.

While there was a lot of hype in the media this year about the Darwin Bicentennial Celebration, Kevin Wirth, ARN Director of Media Relations, found it ironic that a several of the stories on ARN's top ten list this year were articles in scientific journals proclaiming that Darwin's theory should be abandoned because it no longer fits the data, or is severely limited in what it can do or explain. According to
Wirth "a cross disciplinary approach to biology is leading scientists away from reductionistic theories like Darwinian evolution toward more collective, holistic, systems approach." In one of the top ten articles on this topic Mark Buchanan states in Nature Physics "A coming revolution may go so far as to unseat Darwinian evolution as the key explanatory process in biology."

An online version of the ARN Top 10 Darwin and Design stories for 2009 with hyperlinks to original news sources can be found at www.arn.org/top10.

A year ago, Nature published an educational booklet with the title 15 Evolutionary gems (as a resource for the Darwin Bicentennial). Number 2 gem is Tiktaalik a well-preserved fish that has been widely acclaimed as documenting the transition from fish to tetrapod. Tiktaalik was an elpistostegalian fish: a large, shallow-water dwelling carnivore with tetrapod affinities yet possessing fins. Unfortunately, until Tiktaalik, most elpistostegids remains were poorly preserved fragments.

"In 2006, Edward Daeschler and his colleagues described spectacularly well preserved fossils of an elpistostegid known as Tiktaalik that allow us to build up a good picture of an aquatic predator with distinct similarities to tetrapods - from its flexible neck, to its very limb-like fin structure. The discovery and painstaking analysis of Tiktaalik illuminates the stage before tetrapods evolved, and shows how the fossil record throws up surprises, albeit ones that are entirely compatible with evolutionary thinking."

How one of the Devonian animals might have made the tracks (Source BBC News)

Just when everyone thought that a consensus had emerged, a new fossil find is reported - throwing everything into the melting pot (again!). Trackways of an unknown tetrapod have been recovered from rocks dated 10 million years earlier than Tiktaalik. The authors say that the trackways occur in rocks that: "can be securely assigned to the lower-middle Eifelian, corresponding to an age of approximately 395 million years". At a stroke, this rules out not only Tiktaalik as a tetrapod ancestor, but also all known representatives of the elpistostegids. The arrival of tetrapods is now considered to be 20 million years earlier than previously thought and these tetrapods must now be regarded as coexisting with the elpistostegids. Once again, the fossil record has thrown up a big surprise, but this one is not "entirely compatible with evolutionary thinking". It is a find that was not predicted and it does not fit at all into the emerging consensus.

"Now, however, Niedzwiedzki et al. lob a grenade into that picture. They report the stunning discovery of tetrapod trackways with distinct digit imprints from Zachemie, Poland, that are unambiguously dated to the lowermost Eifelian (397 Myr ago). This site (an old quarry) has yielded a dozen trackways made by several individuals that ranged from about 0.5 to 2.5 metres in total length, and numerous isolated footprints found on fragments of scree. The tracks predate the oldest tetrapod skeletal remains by 18 Myr and, more surprisingly, the earliest elpistostegalian fishes by about 10 Myr." (Janvier & Clement, 2010)

The Nature Editor's summary explained: "The finds suggests that the elpistostegids that we know were late-surviving relics rather than direct transitional forms, and they highlight just how little we know of the earliest history of land vertebrates." Henry Gee, one of the Nature editors, wrote in a blog:

"What does it all mean?
It means that the neatly gift-wrapped correlation between stratigraphy and phylogeny, in which elpistostegids represent a transitional form in the swift evolution of tetrapods in the mid-Frasnian, is a cruel illusion. If - as the Polish footprints show - tetrapods already existed in the Eifelian, then an enormous evolutionary void has opened beneath our feet."

In another blog, Ed Yong discussed the significance of the find and is obviously impressed by the endorsement of one seasoned researcher directly involved in trying to understand the evolution of tetrapods:

"Jenny Clack, the Cambridge scientist who discovered Acanthostega, has seen the Polish tracks for herself and finds them more convincing. Her only reservation is that the detailed prints don't have any trackways to show how their maker moved, while the trackways themselves consist of blobs. "But so do lots of previously known tracks," she says. "If you'd found those in other deposits in the last part of the Devonian, you wouldn't have any qualms about them." She'd like to see trackways of the detailed prints but she's nonetheless excited. "It's going to change all our ideas about why tetrapods emerged from the water, as well as when and where.""

Rethinking the why and where is another aspect of this explosive discovery. The first tetrapods have been recognised as animals that lived in water. People have wondered whether fins evolved into legs as the animals negotiated plant material in shallow waters, perhaps brackish or even freshwater. These ideas may still be applicable to Acanthostega and Ichthyostega, but they are not realistic for the new tetrapod trackways - which are found in marine tidal flat sediments.

"Niedzwiedzki and colleagues' apparently anachronistic Eifelian tetrapod trackways will thus shake up thinking about tetrapod origins. They show that the first tetrapods thrived in the sea, trampling the mud of coral-reef lagoons; this is at odds with the long-held view that river deltas and lakes were the necessary environments for the transition from water to land during vertebrate evolution."

The ID interest in this story is for at least two reasons. First, the case documents an example of a failed evolutionary prediction - although, for a while, evolutionists have claimed it as a triumph (see the blog by Casey Luskin on this). Second, the evolution of tetrapods is an important test case for the relevance of design thinking - we ask the question whether tetrapods are here by Design or whether Law+Chance processes are sufficient explanation. Research is proceeding assuming the latter option, but the new discovery suggests that pursuing multiple working hypotheses (including design-based options) might be more prudent.

Tetrapod trackways from the early Middle Devonian period of Poland
Grzegorz Niedzwiedzki, Piotr Szrek, Katarzyna Narkiewicz, Marek Narkiewicz & Per E. Ahlberg
Nature, 463, 43-48 (7 January 2010) | doi:10.1038/nature08623

Abstract: The fossil record of the earliest tetrapods (vertebrates with limbs rather than paired fins) consists of body fossils and trackways. The earliest body fossils of tetrapods date to the Late Devonian period (late Frasnian stage) and are preceded by transitional elpistostegids such as Panderichthys and Tiktaalik that still have paired fins. Claims of tetrapod trackways predating these body fossils have remained controversial with regard to both age and the identity of the track makers. Here we present well preserved and securely dated tetrapod tracks from Polish marine tidal flat sediments of early Middle Devonian (Eifelian stage) age that are approximately 18 million years older than the earliest tetrapod body fossils and 10 million years earlier than the oldest elpistostegids. They force a radical reassessment of the timing, ecology and environmental setting of the fish tetrapod transition, as well as the completeness of the body fossil record.

See also:

Janvier, P. & Clément, G. Muddy tetrapod origins, Nature 463, 40-41 (7 January 2010) | doi:10.1038/463040a

Dalton, R. Discovery pushes back date of first four-legged animal, Nature News, 6 January 2010 | doi:10.1038/news.2010.1

Yong, E. Fossil tracks push back the invasion of land by 18 million years, Not exactly rocket science, January 6, 2010

by Denyse O'Leary
ARN correspondent

(I am an "intelligent design" examiner now. As I have said elsewhere, I don't know how long this will last. Visit if you are interested, and maybe provide some ballast against the flocks of trolls. Apologies for any duplications.)

Intelligent design: What it is

Top ten news events in the intelligent design controversy

Faked embryos are back - at PBS

Some claim that Satan is a great motivator, just like God

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

Darwin landed at the port of Bahia, Brazil, on 28 February 1832. Whilst his writings about the natural history of that part of the world have received much attention, "less well known is the effect Darwin had on the people of Latin America". The effect came through intermediaries - people who were inspired by Darwinism to engineer social change.

The first group of leaders was influential from the late 1880s. They were intellectuals and politicians who had already drank from the wells of secularism. They found Darwin's The Descent of Man compelling and were attracted to the eugenics theorising of prominent Darwinians.

"They soaked up the latest ideas from Europe, and read the works of philosophers such as Herbert Spencer and Francis Galton, Darwin's cousin and the inventor of eugenics. Most Latin Americans thought that society, like nature, evolved from primitive to complex structures, and saw the industrial societies of Western Europe as being more culturally sophisticated than their own."

The secularisation of knowledge in biology was Darwin's most significant achievement, but with it came the conviction that human society needs the same mechanisms (image source here)

Turning this into policy, they promoted mass migration from Europe "to 'whiten' and so 'evolve' their people". They "argued that 'whitening' their nations' stock through interbreeding was the only path to societal improvement". The result was spectacular: more than 11 million immigrants came from Britain, Germany, Ireland, Italy, Portugal and Spain. These people were encouraged to become land owners and to develop leadership roles.

"By 1900, people of European origin dominated society in Argentina and Uruguay. [. . .] European ideas and values spread across Latin America at the expense of Amerindian and African American ones, with the establishment of European-style cities and institutions."

The ideology pendulum swung away from this when the European continent disintegrated in World War I, followed some years after by economic turmoil.

"The death toll of the First World War demonstrated that Europeans had not evolved into superior human beings. A decade later, the Great Depression swept away the export economies underlying modernization in Argentina at least as much as it did in Mexico and Peru, belying the notion that the whitening of the population would lead to permanent social progress."

The intellectuals were still evolutionists at heart, but now it was the Lamarckian sympathies of Darwin that came to the fore.

[These leaders] "followed the 'soft inheritance' notion of French naturalist Jean-Baptiste Lamarck and countered that people's inheritable traits could be changed simply by altering their environment, including their education, diet and living conditions."

These voices came from the "cultural nationalists" who championed the idea of multicultural integration via literacy campaigns with a policy of racial and ethnic blending.

"Although Darwin wasn't specifically invoked in such theories, his body of thought was still influential; so much so that the cultural nationalists might today be described as having adopted their own brand of social Darwinism."

Then came World War II which "dealt a serious blow to notions of human history as a progressive process". Gradual evolutionary change was discarded and the intelligentsia embraced "social revolution as the solution to the region's problems". Although the author of the essay does not link this ideological shift to Darwinism, many communist leaders are known to have looked very favourably on Darwinian concepts. Instead of gradualism, they chose to emphasise survival of the fittest in an amoral world.

Latin America provides us with numerous examples of people taking Darwinian concepts and applying them to the social and political arena. Darwin himself did this in The Descent of Man and his followers have developed these ideas in ways that seem paradoxical today. Some promoted scientific racism and eugenics, whereas others worked for multicultural integration. Some justified capitalism whereas others advocated socialism. Some built their thoughts around gradualism and progress, yet others used survival of the fittest to engineer extinction and social revolution. There is enough in the history of Latin America to make anyone first question and then abandon the principles of Social Darwinism - yet even today there seem to be plenty of scholars who continue to think there is no alternative but to pursue Social Darwinism as the route for structuring social and political philosophy.

"Throughout, Latin America political thinkers shared an optimistic belief that these societies could and would 'evolve' in a positive direction - whatever that direction might be."

Some reflections on these historical developments seem justified.
First, there is an extraordinary malleability in the way Social Darwinism has been expressed. If there is the will, almost every social practice can be given the appearance of scientific respectability. What we do not see are the distinctive characteristics of science: of hypothesis testing, falsification, and the development of theory that can be used to make predictions.
Second, the concept of 'progress', when linked to Darwinism, is a clear indication that there has been an injection of human aspiration. As Darwin conceived his theory, there is no goal (or even a purposeful direction). The evolutionary process is a consequence of Law and Chance, neither of which give support to the "optimistic belief" of politicians about evolving their societies in a "positive direction". These politicians were seeking a place for Design within a theoretical framework that is incompatible with the concept of design. This superimposition of a Design layer on a Law+Chance system has become so widespread that one wonders how intellectuals can live with the incompatibility problem! If the exclusion of Design from evolutionary theory were more widely recognised, would Darwinian ideology be as popular as it appears to be?
This brings us to the third reflection - on subliminal Darwinism. Like the cultural nationalists, many people adopt Darwinism without being conscious of the source of their thinking. They have imbibed a worldview from their peers - without thinking it through for themselves. They are oblivious to the idea that Darwinism is a theory built upon a particular worldview and not just a science of origins. The long-term consequence of this should be cause for concern. Humans are creative, have values affecting behaviour, have a sense of justice and have aspirations. None of these characteristics fit harmoniously with a worldview that is made up of blind, unguided and stochastic processes. That is why many of us are disturbed by attempts to expand the exposure of children to Darwinism in primary school education. Whilst this may be defended by appeals to science, it does little to assuage concerns that what children will get is subliminal indoctrination in a Darwinian worldview.

Global Darwin: Multicultural mergers
Jurgen Buchenau
Nature, 462, 284-285 (19 November 2009) | doi:10.1038/462284a

Abstract: Latin Americans first saw evolution as a reason to 'whiten' their societies, then as a reason to take pride in their mixed lineage, says Jurgen Buchenau in the last of four pieces on Darwin's global influence.

See also:

The Idea of Race in Latin America, 1870-1940, Edited and with an introduction by Richard Graham, with chapters by Thomas E. Skidmore, Aline Helg, and Alan Knight. University of Texas Press, 1990.

Excerpt from Introduction:

Initiated in Europe, the classification and ranking of humankind into inferior and superior races profoundly influenced the development, indeed, the very creation of the sciences. Biology, medicine, psychology, anthropology, ethnology, and sociology were all to some degree shaped by an evolutionary paradigm. The spread of European colonialism and the rapid growth of the United States in the latter half of the nineteenth century brought additional and supposedly irrefutable proof of the validity of a scheme that placed the so-called primitive African or Indian at the bottom of the scale and at its top the "civilized" white European. Many social policies regarding education, crime, health, and immigration were informed by these dominant racial theories. Although the racialist conception of human beings began to lose its credibility from the early twentieth century, it was not until the Nazis began to apply those concepts to eugenics and to undertake massive extermination of the "inferior" races that most scientists firmly denounced the, by then, pseudo-scientific character of racial theories.

For comments on other essays in the Nature series, go here and here.

As reported by ENV...there are two big stories arising from the California Science Center's censorship last October of the pro-intelligent design film Darwin's Dilemma. The first big story, which was the primary focus of a Los Angeles Times article last week, is the act of censorship itself. As an agency of state government in California, the Science Center is required to abide by the First Amendment's guarantee of free speech. The Science Center didn't have to rent its facilities to the public, but once it did so, as a government agency, it was legally obliged by the First Amendment to treat all citizens equally.

But there is another big story tied to the Science Center that hasn't received sufficient attention yet: The Center's illegal cover-up.

The California Science Center has flagrantly violated California's open records law in an apparent effort to hide the real story behind its censorship of Darwin's Dilemma. The Center's evasion of the law is the reason for the open records lawsuit recently brought by Discovery Institute against the Center.

More...

William Dembski and Lewis Wolpert had an audio debate a few weeks ago, which is now available online as a podcast. There is around three minutes of stage-setting by the interviewer Justin Brierly before the actual discussion begins. The debate is part of a program series called UNBELIEVABLE.

Go to podcast...

This is not a book about God, or about intelligent design. Rather, here is a remarkable book, one that dares to challenge natural selection - not in the name of religion but in the name of good science. Most scientists are so terrified of religious attacks on the theory of evolution that it is never examined critically.

But there are major scientific and philosophical problems with the theory of natural selection. Darwin claimed the factors that determine the course of evolution are very largely environmental. This is a thesis that empirical results in biology are increasingly calling into question. The authors show that Darwinism is committed to inferring, from the premise that a kind of creature with a certain trait was selected, the conclusion that that kind of creature was selected for having that trait. Though such inferences are fallacious, they are nevertheless unavoidable within the Darwinist framework. Ultimately, Jerry Fodor and Massimo Piattelli-Palmarini level a devastating critique against Darwinist orthodoxy and suggest new ways of thinking about evolution.

More...

by Denyse O'Leary

ARN correspondent

Here's the contest.

The question arose from my longstanding puzzlement over claims that reptile behaviour could be sharply demarcated from bird or mammal behaviour, according to a tri-partite brain organization. The evidence did not seem to support that. For example, if we use a crude, obvious measure like looking after young, well, many crocodilians (including the Mississippi alligator) are pretty good at it.

Perhaps most reptiles are not. I do not myself plan to conduct a household census among snapping turtles and vipers. But if any species of reptile can do it, the simple three-part claim about the brain seems suspect.

"Aidan" at 3 is the winner, and needs to be in touch with me at oleary@sympatico.ca, to receive his prize.

My only comment is this: If I were a member of a jury that had to decide whether to convict someone of a criminal offence, I would be on my guard immediately when I heard anything about the "reptile brain." So far as I know, if a reptile did it, the reptile's keeper could get a fine for keeping a dangerous animal. That is way less serious than what happens if you are considered morally responsible, instead of unfit to plead, stupid, or something similar.

Meanwhile, I appreciated Collin's comments at 1 and : 2. Re 1: I fear the boy probably did lose his hand/arm or else the use of it, and my purpose in linking to the video was to disadvise foolish stunts with crocodilians. This is unrelated to claims about the "reptile brain" - I would say the same about bears, tigers, or chimpanzees, all of which have inflicted unexpected injuries for no apparent reason. Why risk serious disability to find out that an animal can be unpredictable?

Re 2, it sounds like Collin's in-law is a wise man.

Now here is Aidan's post, a couple of comments interspersed:

The “triune brain” theory (MacLean, 1970) presents the brain in terms of three successive layers:

1) the proto-reptilian system of spinal cord, brain stem, diencephalon and basal ganglia, which controls all genetically-programmed survival behaviours and a range of basic physiological functions such as heartbeat, breathing, digestion, et cetera;
2) the paleo-mammalian ‘limbic’ system, comprised of amygdala, hypothalamus and hippocampus, which generates self-awareness and attendant emotional responses; and
3) the neo-mammalian cerebral cortex, responsible for foresight, insight, reason, speech, et cetera.

MacLean’s model was an attempt to show that the evolutionary inheritance of modern human beings could be directly discerned in the structure of our brains. On the face of it, this seems a reasonable enough approach since, if we are indeed the transitory outcome of an on-going evolutionary process, the evidence ought to be visible within our physiology. As with every evolutionary artefact, however, the theory does not appear to have held up over time and is now outmoded, at least from a neurobiological standpoint. Against the predictions of Maclean’s theory, ‘mammalian’ social and parental behaviours show up in a wide range of non-mammalian vertebrates. Indeed, birds are demonstrably in possession of their own ‘limbic’ structures and reptiles appear to be, too.

[Which is why I would not recommend anyone to interfere with egg-laying vertebrates protecting their eggs, on the theory that those creatures can't - on principle - care - d.*]

The notion of evolution to which the triune theory adheres is ‘pre-synthesis’ – it postulates the addition of novel structure upon novel structure in a linear fashion. The ground of ‘orthogenesis’, however, which presented evolution as steadily progressive, has long since been lost. In the post-synthetic world, those sticking determinedly to evolutionary explanations for the origin and development of life see the process as proceeding mainly through adaptation of pre-existing structures. Three big slabs of systemic independence loosely knitted together would be a crude violation of this, and of the organic interrelatedness of all parts of the brain.

[My own view is that life forms use the brain capacity they have to do their jobs. - d.]

Clinical and ‘pop’ psychologists together and, of course, the lay media, are among those who like the three-brained idea. The concept of mental triplicity does appear to be useful to many people in practice, not as an accurate description of the material organisation of the brain but of the dynamic architecture of the mind as encountered from within. The notion that humans exist upon three ‘planes’ – material, psychic and spiritual – can be found in many traditions and also corresponds to Plato’s tripartite view of the soul. An idea so enduring may well be reflective of something essentially and immutably true.

[Maybe. I don't know. In my experience, "pop" psychologists are looking for "Get out of jail free" cards. "Reptile brain" is as good as the next excuse. We are only beginning the search for real answers.]

(*Note: As a child, I sometimes wandered through swampy areas. One would sometimes be assailed by a male red-winged blackbird- for no apparent reason. Later, it became clear that he was protecting a nest.)

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

Organisms possess a wide variety of strategies for avoiding predation. Crypsis provides a means of avoiding detection; aposematism makes use of warning colouration; mimicry imitates an organism that has better defenses; masquerade "closely resembles inedible and generally inanimate objects". Graeme Ruxton and Michael Speed, who were coauthors of a book on this general theme, have recently coauthored a research paper on masquerade.

"Plants from the genus Lithops look remarkably like stones; stick insects resemble twigs; the Amazon fish Monocirrhus polyacanthus is visually almost indistinguishable from leaves, and birds from the family Nyctibiidae bear an uncanny likeness to tree stumps."

Leaf insects set a high standard for looking like something that's inedible (Credit: (Kirsty Wigglesworth/AP Photo, source here)

My personal favourite examples relate to stick insects and leaf insects. Not only do stick insects resemble the plants on which they live, they sway just as though they are being fanned by a gentle breeze. Furthermore, their eggs look exactly like their own fecal pellets. Newly emerged leaf insects have beautifully formed leafy appendages that allow them to blend in immediately with their surroundings. These characteristics, whilst remarkable, have not been seriously researched:

"one aspect of adaptive coloration has been almost completely ignored: masquerade."

The first research challenge is to determine whether masquerade is a distinctive phenomenon or another form of crypsis. The two relevant hypotheses are:
(a) The predator detects but misidentifies the prey (masquerade)
(b) The predator fails to detect the prey (crypsis)
The researchers set up a set of experiments using domestic chicks as predators and two species of twig-resembling caterpillars. The experimental area contained a hawthorn branch with twigs and leaves. Some experiments were undertaken with a branch that had been bound in purple cotton thread to change its visual appearance.

"Birds with prior experience of twigs took longer to attack both species of twig-resembling caterpillars, and handled them more cautiously, compared with birds that had either no experience of twigs or experience only of twigs whose visual appearance had been manipulated by binding them in colored thread. Our results show that masquerade functions to promote misidentification of the masquerading organism."

Thus far, the authors have demonstrated that hypothesis (a) above is substantiated. Then, in their paper, they proceed with an evolutionary explanation of the phenomenon.

"Our results show that predators' cognitive strategies (recognition and identification), rather than their sensory capabilities, are the selective force driving the evolution of masquerade and raise the possibility that predator cognition may be a more important selective agent than previously realized."

It is a fair conclusion to say that cognitive strategies are significant, as all the birds were able to sense the caterpillars. However, what is the rationale for saying that cognitive strategies have "driven the evolution of masquerade"? Can these experiments tell us anything about the origins of the phenomenon? They tell us that predation is affected by the predator's cognitive strategies, but not that these same strategies have driven the evolution of masquerade as an adaptive response. At best, this is an initial hypothesis awaiting testing. It is a hypothesis based on the assumptions of Darwinism - that masquerade is an adaptation driven by natural selection. To claim this as a conclusion is an indication that theory, rather than data, is dictating the outcome.

The examples of natural selection that we do have fall far short of showing the reasonableness of identifying it as the mechanism for explaining masquerade. We have finch beak length changes, lizard leg length changes, peppered moth colouration, and the like. To demonstrate the reasonableness of explaining masquerade in this way means having multiple factors - including behavioural - all responding to the same selection pressure. Such evidence may be forthcoming but, in the words of the authors (in a different context): "there is certainly no empirical evidence to support this theory". Instead, it is appropriate to propose multiple working hypotheses and proceed to construct ways of testing them. In particular, we can note here the hypothesis that organisms are designed with the potential for radiations linked to adaptive, developmental and epigenetic factors.

Masquerade: Camouflage Without Crypsis
John Skelhorn, Hannah M. Rowland, Michael P. Speed, and Graeme D. Ruxton
Science 327, 1 January 2010: 51.

Abstract: Masquerade describes the resemblance of an organism to an inedible object and is hypothesized to facilitate misidentification of that organism by its predators or its prey. To date, there has been no empirical demonstration of the benefits of masquerade. Here, we show that two species of caterpillar obtain protection from an avian predator by being misidentified as twigs. By manipulating predators' previous experience of the putative model but keeping their exposure to the masquerader the same, we determined that predators misidentify masquerading prey as their models, rather than simply failing to detect them.

See also:

Tyler, D., Stasis in the fossil record of leaf insects, ARN Literature Blog (14 January 2007)

The book, God in Science: An Atheist Defends Intelligent Design by Bradley Monton has been out for five months and has not gone unnoticed by the ID community. In fact, Dr. Monton, a Professor of Philosophy at the University of Colorado-Boulder, is a contributor to ARN. Monton argues that ID is legitimate as a scientific endeavor, although he is unconvinced, at this time, that an intelligent designer exists. It is refreshing to meet up with a clear-thinking, intellectually honest atheist.

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Monton's thinking is blogged in Proslogian by Dr. Jay L. Wile, Nuclear Chemist at the University of Rochester.

Read...

by Denyse O'Leary
ARN correspondent

Here, we asked, as per the title, why do evolutionary psychologists need to debunk compassion?

That's always been a puzzle for me because ... why indeed? Only if one is a slave to basically stupid ideas like "the selfish gene," would debunking compassion, which is widely noted in my local society - and most working societies - seem a worthwhile project. Yet that project generates many useless research papers and other goofy projects.

You'd think more people would be interested in sponsoring compassion than debunking it. But hey.

Anyway, the winner here is Aidan at 6 for this entry (and Aidan needs to get in touch with me at oleary@sympatico.ca with an address to which I can mail the prize):

Proponents of neo-Darwinian orthodoxy are instinctively aware of certain awkward anomalies they need to undermine and contradictions they must cover up if their Big Picture View is to appear to trump all others. In the case of compassion, they are required to show that, whatever else it may be, it isn’t *really* compassion. Compassion as it is – in its raw, undebunked state – is particularly threatening to the materialist worldview because it is a universally accessible and entirely tangible demonstration of the reality of higher orders of being.

True selflessness lies not in the exclusion of oneself but in seeing another person *as* oneself. This is essentially ennobling not only because it rises above self-interest but because, in spirit (and in action), it lifts the other to the precisely same degree as ourselves, to the point where their interests and ours are seen as united within a much greater context. The existentially elevated ground upon which both are then able to stand – ground upon which neither could have stood alone – transcends both the material arrangements of the situation and the confines of each one's personal mentality. Compassion has the power to free us from ourselves and thereby set us upon a very different road.

It is not sympathy, where you suffer along with the person in the hope that this will make them feel better; neither is it pity, where you look down on the person and feel sorry for them from the position of your own safety. As a form of understanding – of oneself, other people and life generally – true compassion is astonishingly rich in content. It is intellectual and spiritual rather than emotional in nature, possessing a power to transform the character beyond recognition. On such a foundation, there is a sense of resonance and alignment with far higher orders, the contours of which we can hardly begin to discern, along with intimations of universal laws profoundly unlike those proposed by materialist observers yet plainly in harmonious accord with laws long since codified by spiritual tradition.

For ideological reasons, materialists and Darwinians cannot allow anything to be in this world that is not of it. If they can show that every instance of compassion fits the grim calculations of one survival strategy or another, they can dismiss every spiritual teaching without further examination. Then they win!

What I liked best about Aidan's entry is that Aidan helpfully distinguishes compassion from mere sentiment - you know what I mean: Blubbing all over someone's sofa about the awful time they are having.

Chances are, the afflicted person secretly wishes that "Blubber" would just go away. Almost any problem is easier to deal with than useless blubbing. Compassion transforms people; blubbing means that the upholsterer must be called in, for advice re the sofa.

Readers in general, never forget the extent to which "evolutionary" psychologists are generally poseurs. I respect the paleontologist who toils in the Badlands or Death Valley. But "evolutionary" psychologists are tax-funded intellectual parasites on a once Big Idea.

Other comments:

Barb, as always, had an excellent comment at 1: This comment particularly struck me:

If materials are solely responsible for morality, as E. O. Wilson asserts, then Hitler simply had bad molecules. He holds no moral accountability for what he did. People not versed in the art of logic and debate as well as those who are Ph.D. candidates in philosophy know this is sheer nonsense.

This comment particularly struck me, because that was one of the motivations for Richard Weikart's involvement in investigating the role of Darwinism in Nazism. The irrational attacks on Weikart for simply documenting the facts were one of my reasons for continuing to follow the story.

qwertyuiop at 4 , I hope you are not running for office anywhere near where I live. Your comments in general, about how materialist mechanist explanations are useful, tell me much. You write,

Would you claim that someone who studies how the brain processes music or the physics of music does not still appreciate music? If not, then why is their seeking of a physical explanation different from “Darwinists and materialists”?

I doubt very much that such a person appreciates music, because they are looking for a debunking explanation. People who get past that can appreciate music - as opposed to being thought well of by fellow members of their herd because they supposedly appreciate music, when all they really offer is a clever putdown.

Here are the contest rules. I gather that I think Contest 19 is still open.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

The title question here riffed off a study that claimed to prove such a point. I must also have been thinking of the "Brights" movement of materialist atheists.

Go here for the original post and all comments.

The winner here is Barb at 2, who needs to provide me with a postal address at which she may receive a copy of The Spiritual Brain. Here is her entry appended, with a couple of comments interspersed:

"Are materialist atheists smarter than other people? How would we know?"

The short answer is no, not really. Paul Johnson wrote a fascinating book entitled Intellectuals, in which essays describe the life courses and contributions of men and women who are considered by most to be of at least above average intelligence. Johnson noted that while these people often did their own thing (so to speak), there is a kind of 'herd mentality' amongst intellectuals. It's as if collective peer pressure stops them from truly speaking their minds. The materialist 'new' atheism espoused today is nothing more than the 'old' atheism with extra doses of rage and hatred towards anything remotely godlike or religious in nature.

[Re the book Intellectuals, I strongly recommend it, as I read it on the advice of a friend. Trust me, you would not want most current cultural icons as advisors.]

Standardized IQ tests could be given, but this would not necessarily prove that materialist atheists are smarter than others, since Daniel Coleman asserts that there are other types of intelligence including emotional and social intelligence that could be used as measuring sticks.

[I think the book meant here is Emotional Intelligence by Daniel Goleman. All concepts of this sort run the risk of descending into fad, though that does not mean that their original insight cannot tell us anything. (I just hope that the [fictional] woman who throws a tantrum at my New Year's party and blubbers all over my living room doesn't go away proclaiming that she is way smarter than the rest of us because she supposedly has "emotional intelligence.")]

What about everyday life? Have the materialist atheists discovered true meaning in their lives? Viktor Frankl wrote that man’s search for meaning is the primary motivational force in one's life. Or are they cogs in a machine, slaving away because their ARM adjusted again and now they're underwater with respects to the mortgage on their house?

[Hard to say, no? My own problem isn't with people who have discovered no meaning in their lives but with people who have discovered a meaning that sounds suspect. Usually, people who have found no meaning are just plain depressed. The others can be all too active in trying to force their "meaning" into reality.]

If they truly are smarter than other people, then they're not in credit card hell making minimum payments, they're not victims of the financial collapse of Wall Street, and they're not gorging on junk food, taking drugs, or engaging in any self-destructive behaviors.

[Well, if that is true of anyone, I am sure glad if they are not demanding that I give them a loan or tax funding. Unfortunately, that actually happens. I'd rather give charity. In some quarters, that is a dirty word, but at least it is a personal relationship.]

Other comments:

Tribune7 at 1 writes, "People who brag about being smart invariably end up losing the hand." If so, I may have done someone somewhere a mercy. Recently, a correspondent wrote me to say that I had helped talk him out of a career in alligator wrestling.

I suppose he would eventually get bored with being called "Lefty."

At 4 toscents asks:

So, who's smarter? The dissembling philosopher, or the mildly demented believer? Does it matter?

Which would you trust with a intimate confession?

Well, it's nice to be asked a question I can actually answer with certainty. I don't need to trust either of them, for the same reason as I do not need to believe either of two implausible stories.

Here are the contest rules. I think Contest 19 is still open.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).